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| The first 32 lines for all of the CHARMM .doc files, in a single document to facilitate searching. |
ace.doc
File: ACE, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Analytical Continuum Solvent (ACS) Potential Purpose: calculate solvation free energy and forces based on a continuum description of the solvent, in particular the analytical continuum electrostatics (ACE) potential. Please report problems to Michael Schaefer at schaefer@brel.u-strasbg.fr WARNING: The module is still being developed and may change in future versions. REFERENCES: M. Schaefer & M. Karplus (1996) J. Phys. Chem. 100, 1578-1599. M. Schaefer, C. Bartels & M. Karplus (1998) J. Mol. Biol., in press. * Menu: * Syntax:: Syntax of the ACE specifications * Defaults:: Defaults and Recommended values * Function:: Purpose of each of the specifications * Examples:: Usage examples of the ACE module File: ACE, Node: Syntax, Up: Top, Previous: Top, Next: Defaults Syntax [SYNTAX ACE functions] Syntax: The ACE specifications can be specified any time the nbond specification parser is invoked, e.g., ENERgy [other-spec] [ace-spec] ace-spec::= [ ACE ] [ IEPS real ] [ SEPS real ] [ ALPHa real ] [ SIGMa real ] File: ACE, Node: Defaults, Up: Top, Next: Function, Previous: Syntax The defaults for the ACE potential are IEPS 1.0 SEPS 80.0 ALPHa 1.2 SIGMa 3.0 In the current implementation, ACE should be used with united atom parameters, ALPHa set equal to 1.2 and the PARAM19 parameter file param19-1.2.inp;adumb.doc
=============================================================================== File: ADUMB, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Adaptive Umbrella Sampling Module Setting up of adaptive umbrella potentials. Currently supported types of umbrella potentials are functions of dihedral angles and functions of the potential energy of the system (energy sampling). WARNING: The module is still being developed and some details are likely to change in future versions. Please report problems to Christian Bartels at cb@brel.u-strasbg.fr REFERENCES: C. Bartels & M. Karplus, J. Comp. Chem. 18 (1997) 1450- C. Bartels & M. Karplus, J. Phys. Chem. 102 (1998) 865- M. Schaefer, C. Bartels, & M. Karplus, J. Mol. Biol. (1998) * Menu: * Syntax:: Syntax of the ADUMB commands * Function:: Purpose of each of the commands * Examples:: Usage examples of the ADUMB module File: ADUMB, Node: Syntax, Up: Top, Previous: Top, Next: Function Syntax [SYNTAX ADUMB functions] Syntax: ADUMb DIHE NRES int TRIG int POLY int 4X(atom-spec) ADUMb ENER NRES int TRIG int POLY int MAXE real MINE real [MAXT real] [MINT real] ADUMb INIT NSIM int [UPDA int] [EQUI int] [TEMP real] [AGIN real] [NEXT int] [THRE real] [UCUN int] [WUNI int] [RUNI int] ADUMb PROB UCUN int [TEMP real] [PUNI int] [TUNI int] ADUMb STON ADUMb STOFf where: atom-spec ::= { segid resid iupac } { resnumber iupac }analys.doc
File: analys, Node: Top, Up: (chmdoc/commands.doc), Next: Description Analysis Commands The ANALysis command is an energy and structure analysis facility that has been developed to examine both static and dynamic properties. The current code allows energy partition analysis and energy contribution analysis from free energy simulations. It also can produce a detailed printout of structural and energy term contributions for selected atoms * Menu: * Description:: Description of analysis facility * Energy:: Energy partitioning File: analys, Node: Description, Up: Top, Previous: Top, Next: Energy Description of the ANALysis Command Syntax: ANALys { ON } { TERM { [ALL] } { NONBond } [UNIT int] atom-selection } { { ANY } { [NONOnbond] } } { OFF } ON Enable energy partition analysis and disable FAST routines. OFF Disable analysis and restore FAST option defaults. TERM Setup energy term print data and disable FAST routines. ALL (default) Print energy terms involving only selected atoms ANY Print energy terms when any of the atoms is selected NONBond In addition to internal terms, also print nonbond terms NONOnbond (default) Do not print electrostatic and vdw energy data UNIT integer Write the energy term printout data to a formatted file Otherwise, write data to the output file. File: analys, Node: Energy, Up: Top, Previous: Description, Next: Top Energy term option of the ANALysis Command The ANALysis ON command enables energy partition analysis and disables the FAST routines. This will slow the calculation (especially on vector machines), but allows a detailed, atom by atom, energy analysis. Everytime the energyaspenr.doc
File: ASPENR, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Atomic Solvation Parameter Based Energy Purpose: calculate solvation free energy and forces based on the exposed surface area of each atom using Atomic Solvation Parameters. Please report problems to brbrooks@helix.nih.gov REFERENCES: M. Wesson and D. Eisenberg, 19??. * Menu: * Syntax:: Syntax of ASP input * Structure:: Structure of the .surf file containing ASP data * Examples:: Usage examples of the ASP module File: ASPENR, Node: Syntax, Up: Top, Previous: Top, Next: Structure Syntax [SYNTAX ASP functions] Syntax: The ASP specifications can be specified any time prior to an energy calculation and can be input either through reading a file or parsed directly off the command line - although the file route is more usual. Once turned on, the ASP energy term is in place during the course of the CHARMM run, i.e., it cannot be turned off except using the skipe command, see *note Skipe (chmdoc/energy.doc). Reading surf file: open unit 1 read vap_to_wat_kd.surf read surf unit 1 close unit 1 File: ASP, Node: Structure, Up: Top, Next: Examples, Previous: Syntax This module computes solvation energies and forces based on the surface area model proposed by Wesson and Eisenberg, i.e., E_solv = Sum (Gamma_i * ASA_i + Eref_i), where Gamma_i is a parameter describing the free energy cost of burying atom i (in units of cal/mol/A^2), ASA_i is the surface area of atom i with radius RvdW_i and probe radius Rprobe and Eref_i is a reference solvation energy. The analytic expressions for atomic surface areas and correspondingblock.doc
File: BLOCK, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The commands described in this section are used to partition a molecular system into "blocks" and allow for the use of coefficients that scale the interaction energies (and forces) between these blocks. This has a number of applications, and specific commands to carry out free energy simulations with a component analysis scheme have been implemented. The lambda-dynamics, an alternative way of performing free energy calculations and screening binding molecules, has also been implemented. Subcommands related to BLOCK will be described here. To see how to output the results of a dynamics run, please see DYNAMICS documentation (keywords are IUNLDM, NSAVL, and LDTITLE). Please refer to PDETAIL.DOC for detailed description of the lambda dynamics and its implementation. BLOCK was recently modified so that it works with the IMAGE module of CHARMM. As some changes to the documentation were necessary anyways, it was decided to also improve the existing documentation. The Syntax and Function section below are relatively unchanged; the added documentation is in the Hints section (READ IT if you are using BLOCK for the first time!). Comments/suggestions to boresch@tammy.harvard.edu. * Menu: * Syntax:: Syntax of the block commands * Function:: Purpose of each of the commands * Hints:: Some further explanations/hints * Limitations:: Some warnings... File: BLOCK, Node: Syntax, Up: Top, Next: Function Syntax of BLOCK commands BLOCk [int] Subcommands: miscellaneous-command-spec ! see *note miscom:(chmdoc/miscom.doc). CALL int atom-selection LAMBda realcadpac.doc
File: Cadpac, Node: Top, Up: (chmdoc/commands.doc), Next: Description Combined Quantum Mechanical and Molecular Mechanics Method Based on CADPAC in CHARMM by Paul Lyne paul@tammy.harvard.edu * Menu: * Description:: Description of the CADPAC commands * Using:: How to run CADPAC in CHARMM * Installation:: How to install CADPAC in CHARMM environment * Status:: Status of the interface code File: Cadpac, Node: Description, Up: Top, Next: Usage, Previous: Top The CADPAC QM potential is initialized with the CADPac command. [SYNTAX CADPac] CADPac [REMOve] [EXGRoup] (atom selection) REMOve: Classical energies within QM atoms are removed. EXGRoup: QM/MM Electrostatics for link host groups removed. The syntax of the CADPAC command in CHARMM follows closely that of the GAMESS command. File: Cadpac, Node: Usage, Up: Top, Next: Status, Previous: Description For complete information about CADPAC input see Chapter 1 in the CADPAC distribution. A QM-MM job using CADPAC needs four input files. The first is the normal CHARMM input file containing the CADPac command. The second file is the CADPAC input file specifying the basis set to be used and the Hamiltonian that is needed. The third and fourth files are libfil.dat and modpot.dat respectively. These are the library and model potential files that are supplied with CADPAC. Cadpac Input File ----------------- For the CADPAC input file the following cards must be present: TITLE, BASIS, ATOMS, RUNTYP, START, FINISH. TITLE: The keyword is always at the start of the input file and is followedcff.doc
^_ File: CFF, Node: Top, Up: (chmdoc/commands.doc), Next: Usage Consistent Force Field (CFF) * Menu: * Usage:: How to use CFF with CHARMM standalone * Status:: Current status of CFF implementation in CHARMM * Theory:: Basis for, parameterization and performance of CFF * Funcform:: Functional form of the CFF energy expression * Refs:: References to papers describing CFF ^_ File: CFF, Node: Usage, Up: Top, Next: Status, Previous: Top In order to use CFF in CHARMM, the user has to issue the following commands: 1. use cff 2. read cff parameter file 3. (a) read rtf name <CFF-capable rtf file>, or (b) read psf name <file_name> 4. read sequence ! if input is via the rtf route (step 3 (a)) 5. generate 6. read coord, or ic build ! if input is via the read rtf/sequence route. When using CFF95 or later Step 3a requires a CFF-capable rtf file. This means a file in which BOND records have been replaced by analogous DOUBLE records for cases in which the chemical structure has a double bond. Note that CFF-capable rtf files are *back compatible*. That is, such rtf files can equally well be used for calculations that utilize the CHARMM force field. Thus, it is *not* necessary to maintain two versions of the rtf files. NOTE: 1. no binary parameter files are supported for CFF. 2. CFF is an all hydrogen force field -- i.e., extended atoms are not supported Examples of CFF usage in CHARMM are given in the ccfftest directory. ^_ File: CFF, Node: Status, Up: Top, Next: Theory, Previous: Usagecfti.doc
File: CFTI, Node: Top, Up: (chmdoc/perturb.doc), Next: Constraints CFTI: conformational energy/free energy calculations * Menu: * Constraints:: Note on constrained optimization implementation * CFTINT:: Description and syntax of standard conformational free energy thermodynamic integration * CFTIM:: Description and syntax of multidimensional onformational free energy thermodynamic integration File: CFTI, Node: Constraints, Up: Top, Previous: Top, Next: CFTINT Constraints: Energy minimization with holonomic constraints has been implemented. There are no special commands for this option. Charlie Brook's TSM module allows for MD simulations with constrained values of selected conformational coordinates - distances, atoms, dihedrals. This has been expanded to also allow energy minimization using several algorithms. The method is an alternative to using harmonic restraints in generating structures of flexible molecules with desired properties, or generating adiabatic profiles. To use this option, simply enter the 'TSM' module and give set of 'FIX' commands to define set of fixed internal coordinates (see perturb.doc for details). Next specify an energy minimization (see minmiz.doc). Algorithms that work: SD, CONJ, POWE (ABNR works also, for reasons unclear to me, KK) File: CFTI, Node: CFTINT, Up: Top, Previous: Constraints, Next: CFTIM CFTI: standard (one-dimensional) conformational thermodynamic integration Description of methodchangelog.doc
File: ChangeLog, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/developer.doc), Next: (chmdoc/parallel.doc) CHARMM Developer's Change Log Entries in each node are recorded by CHARMM developers to indicate new and modified features of CHARMM during the development cycle, i.e., the alpha version period. ------------------------------------------------------ CHARMM22.0.b Release April 22, 1991 CHARMM22.0.b1 Release September 30, 1991 CHARMM22 Release January 1, 1992 c22g1 Release February 15, 1992 c22g2 Release July 7, 1992 c22g3 Release November 3, 1992 c22g4 Release March 1, 1993 c22g5 Release August 1, 1993 CHARMM23.0 c23a1 Developmental August 15, 1992 c23a2 Developmental October 25, 1992 c23f Developmental March 1, 1993 c23f1 Developmental March 15, 1993 c23f2 Developmental August 15, 1993 c23f3 Release February 1, 1994 c23f4 Release August 15, 1994 c23f5 Release March 15, 1995 CHARMM24.0 c24a1 Developmental February 15, 1994 c24x1 Evaluation February 15, 1994 c24a2 Developmental August 15, 1994 c24a3 Developmental March 15, 1995 c24b1 Release August 15, 1995 c24b2 Release February 15, 1996charmm.doc
File: CHARMM, Node: Top Chemistry at HARvard Macromolecular Mechanics - --- - - Version 24b1 - August 15, 1995 Copyright(c) 1984,1987,1991,1994,1995 President and Fellows of Harvard College All rights reserved You are now using the INFO facility to view CHARMM 24 documentation. The paper; CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comp. Chem., Vol. 4, p187 (1983), is considered to be an integral part of this documentation. In places, this documentation and the paper will conflict. In all such cases, the documentation presented here should take precedence. * Menu: * Commands: (chmdoc/commands.doc). Discription and syntax of CHARMM commands * Install: (chmdoc/install.doc). Release notes How to install CHARMM on a user site * Usage: (chmdoc/usage.doc). How to use CHARMM * Support: (chmdoc/support.doc). Supporting data files and utilities * Testcase: (chmdoc/testcase.doc). CHARMM testcases * Develop: (chmdoc/developer.doc). Notes for CHARMM developers * News: (chmdoc/changelog.doc). New features and Modifications * Parallel: (chmdoc/parallel.doc). CHARMM on parallel platforms * Info: (Info). A description of the INFO facility.charmm_gen.doc
File: charmm_gen, Node: Top, Up: (chmdoc/commands.doc), Previous: (chmdoc/install.doc), Next: Configuration The script charmm_gen.com was designed at NIH for easy maintenance of multiple executables in an active research environment. Multiple versions versions can be derived from the same source code, incorporating different features and maximum atom limits. It is assumed that install.com has already been run, and any porting or compiling issues resolved before charmm_gen.com is used. In fact, charmm_gen.com simply calls install.com after doing a little creative copying and renaming. The script is interactive; it asks a few questions, does a lot of checking, and then proceeds to make up to nine different versions in one operation with no further human intervention required. A "test" or development version can also be prepared, and is in fact the "path of least resistance", i.e. the accepting of all the defaults to each prompt. Since simply starting up a LARGE version of CHARMM with most of the available feature sets can easily require 100 Mbyte of memory, we recognized the need to have multiple executables available. Our choice was to create 3 principal versions: "full", with most major modules included; "lite", a version without most of the high memory usage or rarely used modules; and "am1", which adds the QUNATUM QM/MM code and few other features to the "lite" feature set. Each is available in 3 sizes, small, medium, and large. We also use a "cover" script in /usr/local/bin to run CHARMM, after parsing feature set and size keywords, and stripping them from the command line. An example is included at the end of this description. Currently, ten different sets of object libraries are maintained as well; this does require a bit of disk space, but allows rapid re-building of all versions when bugfixes are made. File: charmm_gen, Node: Configuration, Previous: Top, Next: Cover script To use charmm_gen.com, the following additional files are *required* in build/mach, where mach = hpux in this case: Makefile_hpux.gamess Makefile_hpux.nogamess Makefile_hpux.testcommands.doc
File: Commands, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/parallel.doc), Next: (chmdoc/install.doc) CHARMM commands The commands available for use in CHARMM are classified in several groups. * Menu: * Analysis: (chmdoc/analys.doc ). Analysis facility * ACE: (chmdoc/ace.doc ). Analytical Continuum Electrostatics * ADUMB: (chmdoc/adumb.doc ). ADaptive UMBrella sampling simulation * Block: (chmdoc/block.doc ). BLOCK free energy simulation * Cons: (chmdoc/cons.doc ). Harmonic and other constraints or SHAKE * Coordinates: (chmdoc/corman.doc ). Commands to manipulate coordinates * Correl: (chmdoc/correl.doc ). Time series and correlation functions * Crystl: (chmdoc/crystl.doc ). Crystal facility * Dynamics: (chmdoc/dynamc.doc ). Dynamics commands * EEF1: (chmdoc/eef1.doc ). Effective Energy Function 1 * Energy: (chmdoc/energy.doc ). Energy evaluation * Ewald: (chmdoc/ewald.doc ). Ewald summation * GBorn: (chmdoc/genborn.doc ). Generalized Born Solvation Energy * Genetic: (chmdoc/galgor.doc ). The genetic algorithm commands * Graphx: (chmdoc/graphx.doc ). The graphics subsection for workstations * H-bond: (chmdoc/hbonds.doc ). Generation of hydrogen bonds * H-build: (chmdoc/hbuild.doc ). Construction of hydrogen positions * Images: (chmdoc/images.doc ). Use of periodic or crystal environment * Internal: (chmdoc/intcor.doc ). Manipulation of internal coordinates * I/O : (chmdoc/io.doc ). I/O of data structures and files * LonePair : (chmdoc/lonepair.doc). Lone-Pair Facility * LUPOPT : (chmdoc/lupopt.doc ). Low Energy Path OPTimization * MBOND: (chmdoc/mbond.doc ). Multi-body dynamics * MC: (chmdoc/mc.doc ). Monte Carlo simulation program * Minimiz: (chmdoc/minimiz.doc ). Description of the minimization methods * Miscellany: (chmdoc/miscom.doc ). Miscellaneous commands * MMFP: (chmdoc/mmfp.doc ). Miscelaneous Mean Field Potentialcons.doc
File: Cons, Node: Top, Up: (chmdoc/commands.doc), Next: Harmonic Atom CONSTRAINTS The following forms of constraints are available in CHARMM: * Menu: command * Harmonic Atom:: "CONS HARM" Hold atoms in place * Dihedral:: "CONS DIHE" Hold dihedrals near selected values * Internal Coord:: "CONS IC" Holds bonds, angles and dihedrals near table values * Quartic Droplet:: "CONS DROP" Puts the entire molecule in a cage about the center of mass * Fixed Atom:: "CONS FIX" Fix atoms rigidly (sets the IMOVE array) * SHAKE:: "SHAKE" Fix bond lengths during dynamics. * NOE:: "NOE" Impose distance restraints from NOE data * Restrained Distances:: "RESD" Impose general distance restraints * External Forces:: "PULL" Impose externally applied (pulling) force * Sbound: (chmdoc/sbound.doc). Solvent boundary potential File: Cons, Node: Harmonic Atom, Up: Top, Next: Dihedral, Previous: Top Holding atoms in place ------------------------------------------------------------------------------ [SYNTAX CONS HARMonic] Syntax: CONS HARMonic {[ABSOlute] absolute-specs force-const-spec coordinate-spec } { BESTfit bestfit-specs force-const-spec coordinate-spec } { RELAtive bestfit-specs force-const-spec 2nd-atom-selection} { CLEAr } force-const-spec ::= { FORCE real } atom-selection [MASS] { WEIGhting } absolute-specs ::= [EXPOnent int] [XSCAle real] [YSCAle real] [ZSCAle real] bestfit-specs ::= [ NOROtation ] [ NOTRanslation ] coordinate-spec::= { [MAIN] } { COMP } { KEEP }corman.doc
File: Corman, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The Coordinate Manipulation Commands The commands in this section are primarily used for moving some or all of the atoms. There is a wide range of commands and options. All of the commands may be used on either the main coordinate set, or the comparison set. Some commands require both sets of coordinates. * Menu: * Syntax:: Syntax of the coordinate manipulations commands * Simple:: Descriptions of the simple commands * Function:: Descriptions of the remaining commands * Substitutions:: Description and usage of substitution values File: Corman, Node: Syntax, Up: Top, Next: Simple Syntax of Coordinate Manipulation commands [SYNTAX COORdinate manipulation] COORdinates { INITialize } [COMP] [atom-selection] { COPY } [WEIGhting_array] { SWAP } [IMAGes] { AVERage [ FACT real ] } { SCALe [ FACT real ] } { MASS_weighting } { ADD } { SET vector-spec } { TRANslate vector-spec } { ROTAte vector-spec {PHI real} } { {MATRix} } { ORIEnt [MASS] [RMS] [NOROtation] } { RMS [MASS] } { DIFFerence } { FORCe [MASS] } { SHAKe [MASS] } { DRAW draw-spec } { DISTance distance-spec [DIFF] }correl.doc
File: Correl, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Correlation Functions The CORREL commands may be used to obtain a set of time series for a given property from a trajectory. Once obtained, the time series may be manipulated as required, saved or plotted, or to generate correlation functions ( C(tau) = <A(t).A(t+tau)> ). The correlation functions may be manipulated, saved, plotted, and transformed to find spectral density (Fourier transform of C(tau)), etc and determine the correlation times. Alternately, a covariance matrix may be computed for a collection of time series. This option will compute the full matrix for use in entropy calculations or for other applications. Reorienting a coordinate trajectory is possible using the COMPARE command. For details see *note reorient:(chmdoc/dynamc.doc)Merge. * Menu: * Syntax:: The syntax of the correlation command * General:: General information regarding the correlation section * Enter:: How to specify time series * Trajectory:: How to reference to trajectory files * Edit:: How the edit the time series specifications * Mantime:: How to manipulate time series * Corfun:: How to generate correlation functions. * Spectrum:: How to get a spectrum from a correlation function * Cluster:: How to cluster time series data into similar groups * IO:: Input/output guide to correlation functions and series * Examples:: Just what it says File: Correl, Node: Syntax, Up: Top, Previous: Top, Next: General Syntax for the CORREL command and subcommands [SYNTAX CORRelation functions] Syntax: CORREL [ MAXTimesteps int ] [ MAXSeries int ] [ MAXAtoms ] [ COVAriance] - default 512 default 2 default 100crystl.doc
File: Crystl, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Calculations on Crystals using CHARMM The crystal section within CHARMM allows calculations on crystals to be performed. It is possible to build a crystal with any space group symmetry, to optimise its lattice parameters and molecular coordinates and to carry out a vibrational analysis using the options. * Menu: * Syntax:: Syntax of the CRYSTAL command * Function:: A brief description of each command * Examples:: Sample testcases * Implementation:: Background and implementation File: Crystl, Node: Syntax, Up: Top, Next: Function [Syntax CRYStal command] CRYStal [BUILd_crystal] [CUTOff real] [NOPErations int] [DEFIne xtltyp a b c alpha beta gamma] [FREE] [PHONon] [NKPOints int] [KVECtor real real real TO real real real] [VIBRation] [READ] [CARD UNIT int] [PHONons UNIT int] [PRINt] [PRINt] [PHONons] [FACT real] [MODE int THRU int] [KPTS int TO int] [WRITe] [CARD UNIT int] [PHONons UNIT int] [VIBRations] [MODE int THRU int] [UNIT int] xtltyp ::= { CUBIc } { TETRagonal } { ORTHorhombic } { MONOclinic } { TRIClinic }developer.doc
File: Develop, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/testcase.doc), Next: (chmdoc/changelog.doc) CHARMM Developer Guide This is to provide a guide to someone who wants to understand how CHARMM is implemented, and a variety of rules that should be followed by anyone who wishes to modify it. Anyone who wishes to modify CHARMM is advised to read through everything in this document. * Menu: * Implement:: CHARMM Implementation and Management * Directories:: What directories are used to store what information * Standards:: Standards (rules) for writing CHARMM code * Tools:: Tools for CHARMM developers * Modify:: The procedure for modifying anything in CHARMM * Document:: How to document CHARMM commands and features * Checkin:: How to deposit your development version into the central library File: Develop, Node: Implement, Up: Top, Previous: Top, Next: Directories CHARMM Implementation and Management CHARMM is implemented as a single program package, which is developed on a variety of platforms. As a result, it includes some machine specific implementations and makes heavy use of the virtual memory capabilities. By placing everything together, the task of modifying the program is made more reliable because errors in modifying the program are more likely to be noticed. The single source package concept helps us to maintain integrity of CHARMM as the paradigmatic macromolecular research software system running on a variety of platforms. CHARMM was originally written in FLECS, FORTRAN77 and C languages. In the past, before FORTRAN77, FLECS allowed us to use a variety of control constructs, e.g., WHEN-ELSE, WHILE, UNLESS, etc. A FLECS to FORTRAN translator was used to process FLECS source code to produce FORTRAN source. FORTRAN77 provide us some structured language constructs. We began to program directly in FORTRAN77. The initialdynamc.doc
File: Dynamc, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Dynamics: Description and Discussion There are four separate dynamics integrators available in CHARMM: (This discussion does not apply to multi-body dynamics, which has a separate set of integrators). See *note Mbond:(chmdoc/mbond.doc). Name Keyword Module Original Verlet ORIG dynamcv.src Leapfrog Verlet LEAP dynamc.src (default) Velocity Verlet VVER dynamvv.src 4-D L-F Verlet VER4 dynam4.src All methods are based on the Verlet scheme, and when used without any special features, provide identical trajectories for short simulations. All methods allow SHAKE. The ORIG integrator is a standard 3-step Verlet integrator with few frills. It allows: Langevin Dynamics (LANG) Thermodynamic Simulation Method (TSM) The LEAP integrator is similar to the ORIG integrator, but does provide increased accuracy (esp. for single precision version of CHARMM). It allows: Langevin dynamics (LANG) (with accurate temperatures printed) Constant Temperature and Pressure (CPT) (based on Berendsen's method) Accurate pressures with SHAKE High frequency correction to the total energy Parallel code Free energy equilibration indicator (deltaF*V) (with PERT) Thermodynamic Simulation Method (TSM) The VVER integrator also provides increase accuracy. It allows: Constant Temperature (NOSE) (Nose-Hoover method) Multiple Time Step (MTS) The VER4 integrator enables the energy embedding technique that entails placing a molecule into a higher spatial dimension [Crippen, G. M. &eef1.doc
File: EEF1, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Effective Energy Function 1 EEF1 is an effective energy function combining the CHARMM 19 polar hydrogen energy function (with certain modifications, see below) with an excluded volume implicit solvation model. The solvation model is similar in spirit to the Atomic Solvation Parameter approach, but does not use surface areas and is therefore much faster. Latest benchmarks say that simulations with EEF1 take about 50% longer than the corresponding vacuum simulation. The solvation model assumes that the solvation free energy of each group is equal to the solvation free energy of that group in a small model compound less the amount of solvation it loses due to solvent exclusion by other atoms of the macromolecule around it. The exclusion effect of nearest and next-nearest neighbors (1-2 and 1-3 interactions) are neglected because such neighbors also exist in small model compounds. The CHARMM nonbonded atom and exlusion lists are used for the solvation calculation. Because not only DG but also DH and DCp data are available, we can calculate the solvation free energy at different temperatures. This calculation assumes a DCp independent of temperature. Therefore extrapolation to temperatures very different from 300 K is not reliable. EEF1 refers not only to the implicit solvation model but also to the specific modifications and nonbonded options used in CHARMM. The nonbonded options must be: ctonnb 7. ctofnb 9. cutnb 10. group rdie (see example file below). Three files are needed to use EEF1: toph19_eef1.inp : This is a modification of toph19.inp where ionic sidechains and termini are neutralized and contains an extra parameter type (CR)energy.doc
File: Energy, Node: Top, Up: (chmdoc/commands.doc), Next: Description Energy Manipulations: Minimization and Dynamics The main purpose of CHARMM is the evaluation and manipulation of the potential energy of a macromolecular system. In order to compute the energy, several conditions must be met. There are also several support commands which directly relate to energy evaluation. * Menu: * Description:: Description of the energy commands * Skipe:: Selection of particular energy terms * Interaction:: Computation of interaction energies and forces. * Fast:: Requirements for using the fast routines * Needs:: Requirements for all energy evaluations * Optional:: Optional actions to be taken beforehand File: Energy, Node: Description, Up: Top, Next: Skipe, Previous: Top Syntax for Energy Commands There are two direct energy evaluation commands. One is parsed through the minimization parser and the other involves a direct call to GETE. See *note Minimiz:(chmdoc/minimiz.do,,) and *note Gete:(chmdoc/usage.doc)interface. In addition to getting the energy, the forces are also obtained. The ENERgy command. (processed through the minimization parser) [SYNTAX ENERgy] ENERgy [ nonbond-spec ] [ hbond-spec ] [ image-spec ] [ print-spec ] [ COMP ] [ INBFrq 0 ] [ IHBFrq 0 ] [ IMGFrq 0 ] [NOUPdate] hbond-spec *note Hbonds:(chmdoc/hbonds.doc). nonbond-spec *note Nbonds:(chmdoc/nbonds.doc). image-spec *note Images:(chmdoc/images.doc)Update. If the COMP keyword is specified, then the comparison coordinate set is used, but this disables the use of the fast routines. The keyword NOUPdate turns off all update routines, and thus requires all lists to be present already. The GETE command. (a direct call to GETE)ewald.doc
File: Ewald, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax, Previous: Top The Ewald Summation method Invoking the Ewald summation for calculating the electrostatic interactions can be specified any time the nbond specification parser is invoked. See the syntax section for a list of all commands that invoke this parser. Prerequisite reading: nbonds.doc * Menu: * Syntax:: Syntax of the Ewald summation specification * Defaults:: Defaults used in the specification * Function:: Description of the options * Discussion:: More general discussion of the algorithm File: Ewald, Node: Syntax, Up: Top, Next: Defaults, Previous: Top [SYNTAX EWALD] { NBONds } { nonbond-spec } { UPDAte } { } { ENERgy } { } { MINImize } { } { DYNAmics } { } The keywords are: nonbond-spec::= [ method-spec ] { [ NOEWald ] } { } method-spec::= { EWALd [ewald-spec] { [ NOPMewald [std-ew-spec] ] } } { { PMEWald [pmesh-spec] } } ewald-spec::= KAPPa real [erfc-spec] std-ew-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer } pmesh-spec::= FFTX int FFTY int FFTZ int ORDEr integer [QCOR real (***) ] erfc-spec::= { SPLIne { [EWMIn real] [EWMAx real] [EWNPts int] } } { INTErpolate { } } { } { ABROmowitz }fourd.doc
File: Fourd, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax 4 Dimension dynamics: Description and Discussion The energy embedding technique entails placing a molecule into a higher spatial dimension {Crippen,G.M. & Havel,T.F. (1990) J.Chem.Inf.Comput.Sci. Vol 30, 222-227}. The possibility of surmounting energy barriers with these added degrees of freedom may lead to lower energy minima. Here, this is accomplished by molecular dynamics in four dimensions. Specifically, another cartesian coordinates was added to the usual X, Y, and Z coordinates in the LEAPfrog VERLet algorithm. To employ 4D energy embedding, the energy function and force field in CHARMM was modified to include fourth dimension coordinates. An additional harmonic energy function has been included to control the extent to which a molecule is embedded. This is quantatitatively done by altering the value of its force constant, initially given by the parameter K4DI. The 4D energy embedding procedure can be broken down into three parts: 4D coordinate generation, relaxation, and back projection. Fourth dimensional coordinates can be generated in several ways. An energy, E4FILL, in the Fourth dimension can be specified with random coordinates generated as to sum up to the 4D harmonic energy that a user specifies (i.e. E4FILL 50.0 will give coordinates such that the total sums approximately 50.0 Kcal). This method may seem a bit abrupt since a molecule is suddently "thrown" into a higher dimension, hence, molecular dynamics can be used to allow a molecule to more slowly obtain fourth dimension coordinates. This is done by specifying an initial 4D temperature, FSTT4, with subsequent velocities assigned accordingly. Finally, both these methods may be applied simultaneously. Relaxation involves allowing the molecule to explore the potential energy surface and is essentially equilibration. Alternatively, minimization in 4D can be done with the steepest descent algorithm followed by 4D dynamics. Now all that remains is to project this structure back into three dimensions. This last step is thus termed the back projection and is achieved by increasing the fourth dimensional force constant linearlygalgor.doc
File: Galgor, Node: Top, Up: (chmdoc/commands.doc), Next: Implementation Galgor: Commands which deal with Genetic Algorithm and Monte Carlo. # Michal Vieth,H. Daigler, C.L. Brooks III -Dec-15-1997 Initial release. The commands described in this node are associated with genetic algorithm module for conformational searches and docking of small ligands to rigid proteins. The full description of the GA features is presented in the paper "Rational approach to docking. Optimizing the search algorithm" * Menu: * Implementation:: A brief description of the anatomy of GA * Syntax:: Syntax of the replication commands * Description:: Description of key words and commands usage * Restrictions:: Restrictions on usage * Examples:: Supplementary examples of the use of GA File: Galgor, Node: Implementation, Up: (chmdoc/commands.doc), Next: Syntax Genetic Algorithm and Monte Carlo: Description and Discussion Name Keyword Module GA setup GALGOR SETUP genetic.src Genetic algorithm GALGOR EVOLVE genetic.src, genetic2.src Monte Carlo GALGOR EVOLVE MCARLO genetic.src, genetic2.src This code was created by Michal Vieth, Heidi Daigler and Charles Brooks III at The Scripps Research Institute during the summer/fall of 1997 based on the code provided by Charles Brooks and Heidi Daigler, Department of Chemistry, Carnegie Mellon University developed during the summer of 1994. Its purpose is to enable monte carlo and genetic algorithm based conformational searches to be performed on peptides/proteins, small organic molecules and docking of (small) ligands to their receptors. It builds upon the replica ideas of Leo Caves to make multiple copies of the system, i.e., the chromosomes. These chromosomes make up a population of molecular conformations which are crossed and mutated according to the specific genetic algorithm used. It is recomended to use a generational update version of genetic algorithm with elitism 1 or 2, and and island/nicheinggamess.doc
File: Gamess, Node: Top, Up: (chmdoc/commands.doc), Next: Description Combined Quantum Mechanical and Molecular Mechanics Method Based on GAMESS in CHARMM by Milan Hodoscek (milan@par10.mgsl.dcrt.nih.gov,milan@kihp6.ki.si) Ab initio program GAMESS (General Atomic and Molecular Electronic Structure System) is connected to CHARMM program in a QM/MM method. This method is extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990). * Menu: * Description:: Description of the gamess commands. * Using:: How to run GAMESS in CHARMM. * Installation:: How to install GAMESS in CHARMM environment. * Status:: Status of the interface code. * Functionality:: Functionality of the interface code. File: Gamess, Node: Description, Up: Top, Next: Usage, Previous: Top The GAMESS QM potential is initialized with the GAMEss command. [SYNTAX GAMEss] GAMEss [REMOve] [EXGRoup] [QINPut] [BLURred] (atom selection) REMOve: Classical energies within QM atoms are removed. EXGRoup: QM/MM Electrostatics for link host groups removed. QINPut: Charges are taken from PSF for the QM atoms. Charges may be non integer numbers. Use this with the REMOve! BLURred: MM charges are scaled by a gaussian function (equivalent to ECP) Width of the gaussian function is specified in WMAIN array (usually by SCALar command) The value for charge is taken from PSF. Some values of WMAIN have special meaning: WMAIN.GT.999.0 ignore this atom from the QM/MM interaction WMAIN.EQ. 0.0 treat this atom as point charge in the QM/MM potential The atoms in selection will be treated as QM atoms.genborn.doc
File: GBORN, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Generalized Born Solvation Energy and Forces Module The GBORN module permits the calculation of the Generalized Born solvation energy and forces of this energy following a formulation similar to that of Still and co-workers and as described in the manuscript from B. Dominy and C.L. Brooks, III (see below). This module implements the following equation for the polarization energy, Gpol: q q N N i j G = -C (1-1/eps){1/2 sum sum ------------------------------------ } pol el i=1 j=1 [r^2 + alpha *alpha exp(-D )]^(0.5) ij i j ij The gradient of the function is also computed so forces due to solvent polarization can be utilized in energy minimization and dynamics. In its current implementation, the calculation of the alpha(i) variables and the sums over particles indicated in the sums above are done without cutoffs, therefore for large systems these can be costly calculations (though still less so than for explicit solvent). Questions and comments regarding implementation of these equations or there parameterization for the CHARMM forcefields (param19/toph19, param22 for proteins and nucleic acids) should be directed to Charles L. Brooks, III at brooks@scripps.edu. Use of the GB term for MMFF and CFF has recently been implemented and the parameters are given below under examples. The appropriate citation for this work is: B. Dominy and C. L. Brooks, III. Development of a Generailzed Born Model Parameterization for Proteins and Nucleic Acids. J. Phys. Chem., 103, 3765-3773(1999). * Menu: * Syntax:: Syntax of the GBORN Commands * Function:: Purpose of each of the commandsgraphx.doc
File: Graphx, Node: Top, Up: (chmdoc/commands.doc), Next: GRAPHICS Graphics is a subparser of charmm, invoked by via the GRAPH command. All of the miscellaneous commands (miscom.doc), coordinate commands (corman.doc), and internal coordinate commands (intcor.doc) are available from the GRAPHX> prompt. Only the 1st three characters are used for primary graphics commands, but many of the options require the 1st four characters. The graphics facility has been extended to provide general X11 support, and the original Apollo GPR screen display has been dropped; a NODISPLAY version can also be built, which will generate all of the derived files. The other major enhancement is the production of PostScript output files, in either color or grayscale; both X11 and PostScript use the Apollo imaging model. Additional information on X11 usage tips and compiling for X11 are given at the end of this document. Finally, a recent addition is the production of input files for POV-Ray, an excellent freeware ray tracing package for making high quality molecular images. See http://www.povray.org Option keywords are indicated by the use of upper case; lower case terms are variable values, generally real numbers, but decimal points are not required. Triplets ( x y z ) are position dependent; omitted values are assumed to be zero. Items enclosed in square brackets are [optional] but their absence often implies a default choice. Default choices are indicated with an asterisk (*) in syntax listings where apropriate. * Menu: * Summary:: Syntax and Command Summary * Description:: Detailed Command Description with Examples * Output:: PostScript, FDAT, LIGHT, and POV-Ray file formats * Addendum:: X11 Usage and Compiling Tips, Other Useful Programs File: Graphx, Node: Summary, Up: Top, Previous: Top, Next: Description GRAPHX COMMAND SUMMARYhbonds.doc
File: Hbonds, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Generation of Hydrogen Bonds The generation of hydrogen bonds is one of the major steps in analyzing the energy of a system. This energy term is not usually used in minimization or dynamics because modern parameter sets compute hydrogen bond contributions as a balance between electrostatic attraction and van der Waal repulsion terms. This facility remains useful for the purpose of enery and structural analysis. The process of hydrogen bond generation involves looking at all possible pairs of hydrogen bond donors and acceptors and selecting those which are "good". The meaning of "good" is determined by parameters to be described below. In addition, the generation routine is responsible for constructing the positions of all uncoordinated hydrogens and adding them into the coordinate list. The selection of hydrogen bonds involves three checks. First, any good hydrogen bond has a length less than some cutoff. Second, the angle off linearity has a value less than some cutoff. This angle is 180 - D--H...A. Finally, if a hydrogen donor has more than one acceptor which satisfies the above constraints and BEST is specified, the routine will select the one with the lowest energy (normally it will take ALL and let the minimization or dynamics adjust there strengths). To obtain a more detailed description of the selection process and the process of constructing hydrogen coordinates, the CHARMM paper should be consulted. Because there are cutoff's involved with the selection of hydrogen bonds, and because the hydrogen bond list must be updated during dynamics, and because energy must be conserved, switching functions are needed to smooth the transition over a cutoff. Therefore, the specification of hydrogen bond generation also allows the specification of switching function parameters. One should note that particular choices for the selection process will never conserve energy in a dynamics run. First, one must fixhbuild.doc
File: Hbuild, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Construction of hydrogen positions By Axel Brunger, December 1983 * Menu: * Syntax:: Syntax of the HBUILD command * Algorithm:: Description of the used algorithm File: Hbuild, Node: Syntax, Up: Top, Next: Algorithm, Previous: Top Syntax of the HBUILD command [SYNTAX HBUILD] HBUILD [atom-selection] hbond-spec non-bond-spec [PHIStp real] [PRINt] [CUTWater real] [WARN] [DISTof real] [ANGLon real] where <atom-selection> specify the hydrogens to be (re-)constructed (see *note selection:(chmdoc/select.doc).). By default (if no selection is specified) these are all unknown hydrogens and lone pairs (this is equivalent to a selection "SELEction (LONE .OR. HYDRogen) .AND..NOT INITial"). hbond-spec are hydrogen bond specifications, see (*note hbonds:(chmdoc/hbonds.doc)Syntax.) for the detailed syntax, and non-bond-spec are non-bonded interaction specifications, see (*note nbonds:(chmdoc/nbonds.doc)Syntax.) for the detailed syntax. At present the use of the following options is not supported by HBUILD and may yield to errors: BEST in hbond-spec, GROUP [...] in non-bond-spec. PHIStp (default: 10 degrees) determines the step size of the donor group rotation algorithm in HBUILD. PRINt (default: PRINt flag off) if specified prints information about electrostatic, Van der Waals, hydrogen bond, dihedral energy as well as ST2 energy during the performance of the algorithm. If WARN is specified routine ST2WRN is invoked after exiting HBUILD to provide information about unlikely water-(non-polar group)images.doc
File: Images, Node: Top, Up: (chmdoc/commands.doc), Next: Read IMAGES (Original implementation by Bernard R. Brooks, 1983) CHARMM has a general image support system that allows the simulation of almost any crystal and also finite point groups (such as dimers and tertamers...). There is also a facility to introduce bond linkages (with additional energy terms including angles, dihedrals and improper dihedrals) between the primary atoms and image atoms. This allows infinite polymers, such as DNA to be studied. For infinite systems, an assymetric unit may be studied because rotations and reflections are allowed transformations. The IMAGE facility is invoked by reading an image transformation file. From this point, the images of the primary atoms will be included in any energy and force determinations for the remainder of the calculation. A null image file with the INIT keyword will disable this facility. The simple periodic boundary code is underdevelopment by Charles L. Brooks, III at the Scripps Research Institute as of Spring 1995. * Menu: * Read:: Description of the IMAGE data file. * Write:: The write and print options regarding images. * Update:: Options and description of the image update. * Patching:: Specification of image patching. * Centering:: Secification of image centering during updates. * Operation:: Some details and requirements for operation * MIPB:: Minimum Image Periodic Boundary (simple) File: Images, Node: Read, Up: Top, Next: Write, Previous: Top Image Transformation File The IMAGE file contains all of the information needed to define the position and orientation of all symmetric images of the primary atoms. The file is read in free field and may be passed parameters. Syntax:install.doc
File: Install, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/commands.doc), Next: (chmdoc/usage.doc) CHARMM Release and Installation This document contains a formal definition of the current CHARMM release followed by a detailed installation procedure. We concern here features and end-line-user-site installation. Issues regarding developer sites are documented in *note Develop: (chmdoc/developer.doc). * Menu: * Contents:: List of Contents of the current release * Machines:: Machines supported * Install:: Installation Procedure * Documentation:: CHARMM Documentation via emacs INFO program * TOPPAR:: Standard CHARMM Topology and Parameter Files * UserForm:: CHARMM User Group support File: Install, Node: Contents, Up: Top, Previous: Top, Next: Machines CHARMM Release Package The CHARMM release package for CHARMM developers and user sites includes (1) complete source and include files, (2) updated documentation files, (3) some supporting data files, (4) testcases, (5) the PREFX preprocessor and tools needed to set up CHARMM development environments and (6) standard topology and parameter files. The files are organized in the followoing subdirectories. ~/ denotes the directory where you have unpacked (read from a tape drive or issued the UNIX tar command) the CHARMM release package delivered to you. In ~/cnnXm, nn is the version number, X is the version trunk designator (a for alpha or developmental, b for beta release and c for gamma or general release) and m is the revision number. For example, c24b1 is CHARMM version 24 beta release revision 1. ~/cnnXm/ The main directory of CHARMM ~/cnnXm/source/ Contains all CHARMM source filesintcor.doc
File: INTCOR, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The Internal Coordinate Manipulation Commands The commands in this section can be used to construct cartesian coordinates from internal coordinate values. The internal coordinate data structure can also be used for analysis purposes. There are flexible editing commands for manipulating the data structure. When these commands are used in conjunction with the Coordinate Manipulation commands (see *note Corman:(chmdoc/corman.doc).) and the I/O commands (see *note IO:(chmdoc/io.doc).), a rather complete model building facility exists. * Menu: * Syntax:: Syntax of the internal coordinate commands * Function:: Purpose of each of the commands * Structure:: Description of the structure of internal coordinates File: INTCOR, Node: Syntax, Up: Top, Next: Function, Previous: Top Syntax of Internal Coordinates commands [SYNTAX IC - internal coordinate tables] IC { PARAmeters [ALL] } { FILL [COMP] [APPEnd] [PREServe] [SAVEd] } { GENErate [THREe] atom-selection } { DIFFerences [COMP] [APPEnd] [SCALe real] } { DERIvatives [COMP] [APPEnd] [DELTa real] } { DYNAmics dynamics-spec } { EDIT } { BUILd [COMP] [SAVEd] } { SEED atom atom atom [COMP] } { PURGe [SAVEd] } { ADD [SAVEd] } { SUBTract [SAVEd] } { SCALe scale-spec [SAVEd] } { RANDom [ISEEd int] [SAVEd] } { GAUSsian UNIT int atom atom atom }io.doc
File: IO, Node: Top, Up: (chmdoc/commands.doc), Next: Read Input-Output Commands The commands described here are used for reading and writing data structures used in the main part of CHARMM. Some of data structures used in the analysis facility may also be read and written. * Menu: * Read:: Reading data from external sources * Write:: Writing data structures in machine readable form * Print:: Writing data structures in a human readable form on unit 6 * Titles:: Specifying and manipulating titles File: IO, Node: Read, Up: Top, Next: Write, Previous: Top READ - Reads Data from External Sources This command reads data into the data structures from external sources. The external sources can be either card image files or binary files. The fortran unit number from which the information is read, is specified with the unit-spec. The precise format of all these files is described only in the source code as that serves as the only definitive, accurate, and up to date description of these formats. The description of the data structures provides pointers to the subroutines which should be consulted, see *note data: (chmdoc/usage.doc)Data Structures. * Menu: * Read Syntax:: Syntax of the READ command * Sequence:: Reading a segment's sequence * Coordinate:: Reading coordinates * Universal:: Reading coordinates from nonstandard formats * Param files:: The formats used in parameter files * RTF file format:: The format used in topology files * Other files:: Reading all other file types File: IO, Node: Read Syntax, Up: Read, Next: Sequence, Previous: Read Syntax of READ Command [SYNTAX READ]lonepair.doc
File: LonePair, Node: Top, Up: (chmdoc/commands.doc), Next: Description Lone Pair Facility This routine parses the lone-pair command which converts existing atoms to lone-pairs in the PSF. Bernard R. Brooks, NIH, October, 1997 * Menu: * Syntax:: Syntax of the lone-pair command * Description:: Description of the lone-pair facility File: LonePair, Node: Syntax, Up: Top, Previous: Top, Next: Description Syntax of the Lone-Pait Command [SYNTAX LONEpair] LONEpair { FIXEd atom-spec [ xloc-yloc-zloc ] } [MASS] { } { CENTer atom-spec { atom-selection } } { { repeat(atom-spec) } } { } { COLOcate { 2x(atom-selection) } } { { 2x(atom-spec) } } { } { { COLInear distance-spec } { 3x(atom-selection) } } { { CEN2 } { 3x(atom-spec) } } { } { { RELAtive } { 4x(atom-selection) } position-spec } { { BISEctor } { 4x(atom-selection) } } { { CEN3 } } { } { PRINt } { CLEAr } atom-spec::= { residue-number atom-name } { segid resid atom-name } { BYNUm atom-number } atom-selection ::= see *note select:(chmdoc/select.doc).lupopt.doc
File: LUPOPT, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Low Energy Path OPTmization This method optimizes a low energy path between a series of molecular structures. Energy minimization is done with constraints on center of mass translation, rotation and orthogonality of step to path vector. Reference : Choi, C. and Elber, R., J. Chem. Phys. 94:751 (1991) Source Code : rxncor/lupopt.src Krzysztof Kuczera, 12-Mar-1997, Lawrence, KS. * Menu: * Syntax:: Syntax of the LUPOpt command * Description:: Description of the keywords and options for setting up the low energy path calculation. * Memory:: Memory Requirements File: LUPOPT, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for the LUPOpt Command LUPOpt [NPATh integer] [UOUT integer] [INIT integer] - [EPSEner real] [MAXCycle integer] [STEP real] [IPVOpt integer] - [LPrint integer] [for 'INIT 2' this line should be followed directly by NPATH lines containing names of formatted CHARMM COOR files, no blank lines] Variable Default Meaning NPATH MXPATH Number of path points UOUT 21 Unit number for output trajectory with optimized path INIT 1 Initialization mode: =1 - straight line in Cartesian space from MAIN to COMP coordinates =2 - read path from set of files, file names supplied below, 1 per line, no blank lines EPSE 0.001 Structure will be classified as converged ifmbond.doc
File: Mbond, Node: Top, Up: (chmdoc/dynamc.doc), Next: Dynamic Multi-body Dynamics: Overview In multi-body dynamics, aggregates of atoms are gathered into "bodies". For a dynamics run, the system comprises one or more bodies and zero or more atoms which are not part of any body. By gathering the atoms in this way, the total number of variables in the system is considerably reduced which is expected to significantly improve the computational performance. Furthermore because such a simulation aims to reproduce the characteristic (i.e. low-frequency) motion of the system, relatively long time steps are possible. The final advantage of this scheme is that bond-lengths may be explicitly constrained (between bodies and in the atomistic regions) in a computationally efficient manner. There are two steps needed before starting a dynamics run Identifying the bodies and the atomistic regions and Generating (or loading pre-calculated) modes for each of the bodies. All of the standard CHARMM output and analysis mechanisms work with multi-body dynamics. One new file format is used (to store computed mode shapes). The MBOND command is used for setting up the system and controlling its activation. It can be used either as a single line command (mainly for control and status reports) or as an opening for a command block (for setting up the system substructuring and mode assignments). All the single line commands can be also used from within the command block. The single line commands are: MBOND { [ON ] } { [OFF ] } { [CLEAr ] } { [STATus { [SHORt ]} ]} { [LONG [BODY char*4] ]}mc.doc
File: mc, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Monte Carlo The Monte Carlo commands in CHARMM have been designed to allow construction and use of an almost arbitrary move set with only a few atom selections. This goal is accomplished by providing a pre-defined set of move types which can be combined to specify the allowed movements of an arbitrary CHARMM molecule. Speed and flexibility are gained by separating the bookkeeping associated with a move (MOVE subcommands) from the actual application of that move to the molecule (MC). * Menu: * Syntax:: Syntax of MOVE and MC commands * Description:: Description of MOVE and MC commands * Examples:: Examples of MOVE and MC commands * Data Structures:: Data structures shared by the MOVE and MC commands * Shortcomings:: Known problems and limitations * References:: Some references of use File: mc, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for MOVE and MC commands [Syntax MOVE < ADD | DELEte | EDIT | READ | WRITe > ] MOVE ADD 1{ MVTP move-type } nsele{ SELE...END } - [ WEIGht 1.0 ] [ DMAX 1.0 ] - [ ARMP -1.0 ] [ ARMA 0.0 ] [ ARMB 0.0 ] - [ DOMCf -1.0 ] [ ANISotropic 0 ] - [ FEWEr 0 ] [ NLIMit 1 ] [LABEL move-label ] where nsele, the number of SELE...END statements, depends on move-type move-type (nsele)::= < RTRN rig-unit ( 1 ) | ! Rigid translations RROT rig-unit ( 1+) | ! Rigid rotations CART ( 1 ) | ! Single atom Cartesians TORS ( 2 ) | ! Simple torsion rotations CROT ( 1+) > ! Concerted torsion rotationsminimiz.doc
File: Minimiz, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Energy Manipulations: Minimization and Dynamics One can minimize the energy by adjusting the coordinates of all the atoms in order to reduce its value. Several minimization algorithms are provided. They include; Steepest Descents (SD) Conjugate Gradient (CONJ) Adopted Basis Newton-Raphson (ABNR) Newton-Raphson (NRAP) Powell (POWE) Truncated Newton Method (TNPACK) * Menu: * Syntax:: Syntax of the energy manipulation commands and a table of keywords * Description:: Description of the various keyword functions * Discussion:: Discussion of the various methods File: Minimiz, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for Energy Manipulation Commands [SYNTAX MINImize] MINI { SD } [ nonbond-spec ] [ hbond-spec ] - { CONJ conj-spec } [ INBFrq 0 ] [ IHBFrq 0 ] [NOUPdate] { ABNR abnr-spec } { NRAP nrap-spec } { POWEll } { TN tnpack-spec } [STEP real] [GRADient] [DEBUg] [ frequency-spec ] [ tolerence-spec ] [ print-spec ] } hbond-spec::= *Note Hbonds:(chmdoc/hbonds.doc). nonbond-spec::= *Note Nbonds:(chmdoc/nbonds.doc). frequency-spec::= [NSTEP int] [IHBFrq int] [INBFrq int] [NPRInt int] tolerence-spec::= [TOLENR real] [TOLGRD real] [TOLITR int] [TOLSTP real] print-spec::= [IMAXp int] [IPRInt int] [PRTMin int]miscom.doc
File: MISCOM, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Miscellaneous Commands The commands described in this section are generally more simple in nature than those of previous sections. Some are perhaps obsolete, but included for the sake of completeness. * Menu: * Syntax:: Syntax of the miscellaneous commands * Function:: Purpose of each of the commands File: MISCOM, Node: Syntax, Up: Top, Next: Function, Previous: Top Syntax of miscellaneous commands --------------------------------------------------------------------------- File handling: OPEN UNIT integer NAME filename [WRITe ] [UNFORMatted] [READ ] [FILE] [APPEnd] [FORMatted] [CARD] LOWEr ! Force the case of output file names UPPEr ! " CLOSe UNIT integer [DISPosition KEEP ] [DISPosition DELEte] REWInd UNIT integer INQUire ! get a list of open files and their qualifiers, only from CHARMM ! possible STREam [ UNIT integer ] [ repeat(argument) ] [ file_specification ] ! Call another input file OUTUnit integer ! Redirect output to a different unit. RETUrn ! Return to the previous unit --------------------------------------------------------------------------- DEFIne keyname SELE atom_selection END SYSTem "shell-cmd" ! Execute a shell command (Unix) STOP ! Terminate CHARMM USER .... ! Invoke a user supplied subroutine (USERSB)mmff.doc
File: MMFF, Node: Top, Up: (chmdoc/commands.doc), Next: Usage Merck Molecular Force Field (MMFF94) * Menu: * Usage:: How to use MMFF with CHARMM standalone * Quanta:: How to use MMFF from QUANTA * Status:: Current status of MMFF implementation in CHARMM * Theory:: Basis for, parameterization and performance of MMFF94 * Funcform:: Functional form of the MMFF energy expression * Refs:: References to papers describing MMFF94 * Parameters:(chmdoc/mmff_params.doc). MMFF Parameters File: MMFF, Node: Usage, Up: Top, Next: Quanta, Previous: Top In order to use MMFF in CHARMM, the user has to issue the following commands: 1. use mmff force field 2. <read mmff parameter files> 3. (a) read rtf name <MMFF-capable rtf file>, or (b) read merck name <file_name> 4. read sequence ! if input is via the rtf route (step 3 (a)) 5. generate ! note that there may be multiple segments in one .mrk file 6. patch ! if input is via rtf/sequence route, apply appropriate patches ! to force a new mmff_setup; either include the keyword "mmff" ! on the final patch or follow the final patch by the command: ! "use mmff atom types" 7. read coord, or ic build ! if input is via the read rtf/sequence route. Steps 1 & 2 can be done by streaming the file "mmff_setup.STR." An example of this file is shown below. Documantation on the contents and usage of the MMFF parameter files may be found in mmff_params.doc. Step 3a requires a MMFF-capable rtf file. This means a file in which BOND records have been replaced by analogous DOUBLE or TRIPLE records for cases in which the chemical structure (or any valid Kekule representation) has a double or triple bond. Mass records in a MMFF-capable rtf file must also be augmented to add the atomic symbol for each CHARMM atom typemmff_params.doc
File: MMFF_PARAMS, Node: Top, Up: (chmdoc/mmff.doc), Next: MMFFSYMB The MMFF94 Setup Procedure And Parameter Files * Menu: * MMFFSYMB:: The MMFFSYMB.PAR file (symbolic atom types) * MMFFAROM:: The MMFFAROM.PAR file (aromatic atom types) * MMFFHDEF:: The MMFFHDEF.PAR file (atom types for hydrogens) * MMFFDEF:: The MMFFDEF.PAR file (numeric atom types) * MMFFPROP:: The MMFFPROP.PAR file (properties of MMFF atom types) * MMFFBOND:: The MMFFBOND.PAR file (bond-stretching parameters) * MMFFBNDK:: The MMFFBNDK.PAR file (empirical-rule bond parameters) * MMFFANG:: The MMFFANG.PAR file (angle-bending parameters) * MMFFSTBN:: The MMFFSTBN.PAR file (stretch-bend parameters) * MMFFDFSB:: The MMFFDFSB.PAR file (empirical-rule str-bend parameters) * MMFFOOP:: The MMFFOOP.PAR file (out-of-plane bending parameters) * MMFFTOR:: The MMFFTOR.PAR file (torsion partameters) * MMFFVDW:: The MMFFVDW.PAR file (van der Waals parameters) * MMFFCHG:: The MMFFCHG.PAR file (bond-increment "charge" parameters) * MMFFPBCI:: The MMFFPBCI.PAR file (empirical-rule charge paramters) * MMFFSUP:: The MMFFSUP.PAR file (supplementary MMFF parameters) File: MMFF_PARMS, Node: MMFFSYMB, Up: Top, Next: MMFFAROM, Previous: Top 1. MMFFSYMB.PAR. Starting from the input atomic species, connectivity, and formal bond orders (for aromatic systems, for example, a Kekule structure having alternating single and double bonds must be supplied), the MMFF structural perception code automatically "sets up" the calculation by perceiving and classifying rings, detecting aromaticitity, and creating appropriate lists of bond, angle and torsional interactions. The atom typing procedures (currently overseen by subroutines XTYPE, HTYPE and RGTYPE) then assign a 4-character symbolic atom type to each atom. Finally, the entries in MMFFSYMB.PAR are used to translate the symbolic atom types into the numeric atom types actually employed in assigning force-field parameters to the force-field interaction terms. Note that this is a many-mmfp.doc
File: MMFP, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The Miscelaneous Mean Field Potential (MMFP) Commands The commands in this section are primarily used for setting up special restraining potentials on some or all of the atoms. The key word MMFP is used to enter the MMFP environement. In the MMFP environment, all miscelaneous commands (label, goto, if, etc...), and string substitutions (with @1, @2, etc...) are supported. The key word END returns to the main parser. The restraining potentials are used in all energy calculations, unless SKIP is used (see *note select:chmdoc/energy.doc). The subcommand RESET clears the potential. This module is still under developement and only the subcommand GEO is released. The subcommand GEO (standing for geometrical) is used to setup various restraining potential (spherical, planar or cyclindrical restraints) on some or all atoms. The selection specification should be at the end of the command. The default atom selection includes all atoms. Future subcommands will include continuum electrostatic reaction field and solvent mean field potentials. Expected date of release is Spring 1994. * Menu: * Syntax:: Syntax of the MMFP commands * Details:: Descriptions of the GEO subcommands * Examples:: Examples of GEO subcommands * Substitutions:: Description and usage of substitution values File: MMFP, Node: Syntax, Up: Top, Previous: Top, Next: Details Syntax of basic MMFP commands GEO reset GEO [maxgeo INTE] [shape_specification] [position_spec] [RCM] [potential_spec] [atom_selection] [ DISTANCE atom_selection] SSBP reset SSBP [atom_selection] [atom_selection] [ssbp_specification] BHEL [atom_selection] SHEL [atom_selection] [shell_options-specification] shape_specification:== { [SPHERE] } [XREF real] [YREF real] [ZREF real]molvib.doc
File: Molvib, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax The MOLVIB Module of CHARMM By K.Kuczera & J.Wiorkiewicz-Kuczera, May 1991 MOLVIB is a general-purpose vibrational analysis program, suitable for small to medium sized molecules (say of less than 50 atoms). For larger systems the detail of description may be too great. The main options are: - the vibrational problem in internal coordinates (GF) - the vibrational problem in cartesian coordinates (GFX) - analysis of GAUSSIAN program output (GFX,GAUS) - analysis of dependencies in internal coordinate sets (G) - canonic force field calculations (KANO) - crystal normal mode analysis for k=0 (CRYS) - generating cartesian displacements along some interesing directions (STEP) The different options use mostly the same package of subroutines called in different order. New applications may thus be easily added when necessary. Of special interest is the symbolic PED analysis package, enabling a clear and condensed overview of the usually complex PED contributions. * Menu: * Syntax:: Syntax of the MOLVIB command * Function:: Purpose of each of the keywords * Input:: MOLVIB Input Description File: Molvib, Node: Syntax, Up: Top, Previous: Top, Next: Function [SYNTAX MOLVib command] MOLVib NDI1 int NDI2 int NDI3 int [NATOm int] [MAXSymbol int] [NGMAx int] [NBLMax int]monitor.doc
File: Monitor, Node: Top, Up: (chmdoc/dynamc.doc), Previous: (chmdoc/dynamc.doc), Next: Syntax Monitor commands: Commands to monitor various dynamics properties * Menu: * Syntax:: Syntax of the Monitor commands * Properties:: Description of the properties monitored File: Monitor, Node: Syntax, Up: Top, Next: Properties, Previous: Top [SYNTAX MONItor dihedral transitions] Syntax of the MONItor commands MONItor {DIHEdral} [SHOW] FIRSt unit-number NUNIt integer BEGIn integer - STOP integer SKIP integer [SELEct atom-selection] FIRSt the unit number of the first file of dynamics coordinate sets from which the property is to be calculated. NUNIt the number of units of dynamics coordinate files. Fortran unit numbers must be assigned to the files consecutively from FIRST. BEGIn the first step number for the coordinate set from which the property will be calculated. STOP the last step number for the coordinate set from which the property will be calculated. SKIP the time increment between the step numbers of the coordinates. SELEct selected atoms for which the property is to be monitored. At this time, atoms may be selected only by the atom-selection keywords (e.g. RESID,TYPE,ATOM,RESN,SEGID) and NOT by tag-selections. (see *note select:(chmdoc/select.doc).) DIHE Property: monitor the dihedral transitions. SHOW for monitoring dihedral transitions, print out the step number, the cumulative number of transitions, the dihedral name, the current dihedral angle, and the old and new minimum well positions each time a transition is found. ALL Lots of printout. UNIT Unit number to write results (default: outu) File: Monitor, Node: Properties, Up: Top, Previous: Syntax, Next: Top Properties monitored using the MONItor commandsmts.doc
File: MTS, Node: Top, UP: (chmdoc/dynamc.doc), Previous: (chmdoc/dynamc.doc), Next: Syntax **************************************** * Multiple Time Scales Method (MTS) * **************************************** In CHARMM, multiple time scales method (MTS) algorithm is similar to code of the algorithm described in the paper by Tuckerman, Berne, and Martyna [J.C.P., 97, 1990 (1992)]. Please refer to this paper for details of derivations of this MTS-RESPA method. In addtion, more details can be seen in J. Chem. Phys. 99, 8063 (1993) and J. Phys. Chem., 99, 5680 (1995) by M. Watanabe and M. Karplus. In this new release, MTS method can be called under parallel platforms. All modules under MTS should work in parallel. To run CHARMM in parallel, please refer to parallel.doc. The MTS method can be combined with Langevin dynamics via the LN algorithm, described by Barth and Schlick [J.Chem.Phys., 1998, in press]. This version includes the slow forces via extrapolation and is expected to allow larger timesteps than reversible MTS-RESPA. See general notes at the end of this documentation file. LN algorithm was implemented in CHARMM by Eric Barth (8/97) and Adrian Sandu (7/98). In this documentation we refer to the rRESPA code as MTS-RESPA (performing Newtonian dynamics) and to the LN code as MTS-LN (performing Langevin dynamics). *Menu: * Syntax:: Syntax of the MTS dynamics command * Desc:: Description of the keywords and options * Note:: Energy routines and MTS method selections * Exam:: Example of Multiple Time Scale Method File: MTS, Node: Syntax, Up: Top, Next: Desc, Previous: Top **************************************************** * Syntax for the Multiple Time Scaled Method (MTS) * **************************************************** In this Multiple Time scaled method in CHARMM, a reversible RESPAnbonds.doc
File: Nbonds, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Generation of Non-bonded Interactions Nonbonded interactions (frequently abreviated "nbond") refer to van der Waals terms and the electrostatic terms between all atom pairs that are not specifically excluded from nonbond calculations as for example are directly bonded atoms *note nbx: (chmdoc/struct.doc)nbx. These terms are defined on atom pairs and to a first aproximation would require the number of atoms squared calculations. To avoid this burden various truncation and approximation schemes can be employed in the program, breaking the nonbonded calculation into two parts, initialization and actual energy calculation. The method of approximation, cutoffs, and other relevant parameters can be entered any time the nbond specification parser is invoked. See the syntax section for a list of all commands that invoke this parser. * Menu: * Syntax:: Syntax of the nonbond specification * Defaults:: Defaults used in the nonbond specification * Function:: Description of the options * Tables:: Using nonbond lookup tables in place of analytic potential energy functions * Cubes:: Alternative way to compute the nonbonded ontact list * Cluster:: Cube-Cluster nonbonded list generation method File: Nbonds, Node: Syntax, Up: Top, Next: Defaults, Previous: Top [SYNTAX NBONDs] { NBONds } { [INBFrq integer] nonbond-spec } { UPDAte ... } { } { ENERgy ... } { } { MINImize ... } { } { DYNAmics ... } { } { VIBRAN ... } { } { CORRel ... } { }nmr.doc
File: NMR, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax NMR Analysis Module The NMR commands may be used to obtain a set of time series for a number of NMR properties from a trajectory. Among the possible properties are relaxation rates due to dipole-dipole fluctuations (T1, T2, NOE, ROE), chemical shift anisotropy and Deuterium order parameters for oriented samples. The documentation assumes that users are already familiar with NMR. Several textbooks are available for users interested in more information. The NMR command invokes the NMR subcommand parser. Because several properties are based uppon the position of nuclei that may not have been included in the PSF (and the trajectory) the module has its own building submodule (see BUILD) to construct atoms. For example, the H_alpha on the C_alpha can be constructed without invoking HBUILD for T1 and T2 calculations. Everthing is stored on the HEAP and no variables are kept when the module is left (there is no nmr.fcm common block). Everything is re-initialized when the module is exited with the END command. WARNING: The module has not been used in numerous situations and caution should be the rule. All problems should be reported to Benoit Roux at rouxb@ERE.Umontreal.CA, phone (514) 343-7105. * Menu: * Syntax:: Syntax of the NMR commands * Function:: Purpose of each of the commands * Examples:: Usage examples of the NMR analysis commands File: NMR, Node: Syntax, Up: Top, Previous: Top, Next: Function Syntax [SYNTAX NMR functions] Syntax: NMR enter the NMR module END exit the NMR module Subcommands:nose.doc
The documentation of Nose-Hoover method - Masa Watanabe ----------------------------------------------------------------------- File: Nose, Node: Top, Up: (chmdoc/dynamc.doc), Previous: (chmdoc/dynamc.doc), Next: Syntax ********************************************** * Nose-Hoover Molecular Dynamics command * ********************************************** This module offers access to the Constant-Temperature molecular dynamics defined by Nose-Hoover equations of motion (described in S.Nose JCP, 81 P511 (1984) and W.G. Hoover, Phy. Rev. A31, p1695 (1985)) This method has the advantage that it is a continuous dynamics with well defined conserved quantities. [Other temperature scaling methods, available in CHARMM (included Berendsen method in Leap-frog integrator) have discontinuous dynamics.] *Menu: * Syntax:: Syntax of the Nose-Hoover command * Main:: Nose-Hoover method main commands and descriptions * Exam:: Example of Nose-Hoover Method File: Nose, Node: Syntax, Up: Top, Next: Main, Previous: Top ************************************** * Syntax for the Nose-Hoover Command * ************************************** The original Hamiltonian for Nose dynamics is defined as follow: H = H0 + HB = H0(p/s,q) + P^2/2Q + (f+1)kTlns (1) where f is a degree of freedom of the physical system. This Hamiltonian was originally propoesed by Nose in his JCP paper. The equations of motions defined by Eq. (1) are solved numerically in order to achieve the canonical ensemble MD simulation. Hoovers extended the Nose's analysis. He derives a slightly different set of equations of motions which dispense with the time-scaling parameter s by transforming p' = p/s, S = lns and dt' = dt/s. Then he define the conserved quantity: H = H0(p',q) + P^2/2Q + (f+1)kTS (2)parallel.doc
This is Info file parallel.doc, produced by Makeinfo-1.61 from the input file parallel.texi. File: Parallel, Node: Top, Up: (chmdoc/charmm.doc), Next: (chmdoc/commands.doc), Prev: (chmdoc/changelog.doc) Parallel Implementation of CHARMM CHARMM has been modified to allow computationally intensive simulations to be run on multi-machines using a replicated data model. This version, though employing a full communication scheme, uses an efficient divide-and-conquer algorithm for global sums and broadcasts. Curently the following hardware platforms are supported: 1. Cray T3D/T3E 7. Intel Paragon machine 2. Cray C90, J90 8. Thinking Machines CM-5 3. SGI Power Challenge 9. IBM SP1/SP2 machines 4. Convex SPP-1000 Exemplar 10. Parallel Virtual Machine (PVM) 5. Intel iPSC/860 gamma 11. Workstation clusters (SOCKET) 6. Intel Delta machine 12. Alpha Servers (SMP machines, PVMC) 13. TERRA 2000 14. HP SMP machines 15. Convex SPP-2000 16. SGI Origin 17. LoBoS (any Beowulf) * Menu: * Installation:: Installing CHARMM on parallel systems * Running:: Running CHARMM on parallel systems * PARAllel:: Command PARAllel controls parallel communication * Status:: Parallel Code Status (as of September 1998) * Using PVM:: Parallel Code implemented with PVM * Implementation:: Description of implementation of parallel code File: Parallel, Node: Installation, Next: Running, Prev: Top, Up: Top For support of many parallel comunication libraries the CMPI keyword was added. In order to get the old communication routines always specify CMPI otherwise MPI is the default choice (see recommended keyword combination for each specific platform). On some platforms recommended preflx directives prepare the code which does the communication much faster, eg on 128 nodes T3E CMPI is 4 times fasterparmfile.doc
File: Parmfile, Node: Top, Up: (chmdoc/commands.doc), Previous: (chmdoc/usage.doc)Standard Files, Next: Overview CHARMM Emprical Energy Function Parameters This section describes parameters in the CHARMM empirical energy function. * Menu: * Overview:: Overview of CHARMM parameter file by A. D. Mackerell Jr. * Multiple:: Rules for the use of multiple dihedrals in CHARMM22 * Conversion:: Rules for conversion of old nucleic acid rtf and param to CHARMM22 format * PARMDATA:: Description of Parameter Files available for general use. File: Parmfile, Node: Overview, Up: Top, Previous: Top, Next: Multiple Overview of CHARMM parameter files By Alexander D. MacKerell Jr., July 1997 This section of the documenation contains a brief description of the contents of a parameter file. The CHARMM parameter file contains the information necessary to calculate energies etc. when combined with the information from a PSF file for a structure. Information on the keywords found in the parameter file is in IO.DOC. (A) * CHARMM example parameter file * (B) BOND H O 500.0 1.00 (C) ANGLe (THETa) H O H 100.0 104.51 20.0 1.70 (D) DIHEdral (PHI) HT CT CT HT 10.0 3 180.0 X CT CT X 10.0 3 180.0 (E) IMPH O C CT N 5.0 1 0.0 X C CT X 5.0 1 0.0 X X CT N 5.0 1 0.0 O X X N 5.0 1 0.0pbeq.doc
File: PBEQ, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Poisson-Bolztmann Equation Module The PBEQ module allows the setting up and the numerical solution of the Poisson-Boltzmann equation on a discretized grid for a solute molecule. WARNING: The module has not been used in numerous situations and caution should be the rule. All problems should be reported to . Benoit Roux at rouxb@PLGCN.Umontreal.CA, phone (514) 343-7105 . Dmitrii Beglov at beglovd@PLGCN.Umontreal.CA . Wonpil Im at imwo@PLGCN.Umontreal.CA * Menu: * Syntax:: Syntax of the PBEQ commands * Function:: Purpose of each of the commands * Examples:: Usage examples of the PBEQ module File: PBEQ, Node: Syntax, Up: Top, Previous: Top, Next: Function Syntax [SYNTAX PBEQ functions] Syntax: PBEQ enter the PBEQ module END exit the PBEQ module Subcommands: SOLVe convergence-specifications grid-specifications physical variable-spec. boundary potential-spec. membrane-specifications spherical droplet-spec. cylinder-specifications dielectric boundary-spec. force-specifications charge interpolation-spec. atoms-selection ITERate convergence-specifications ENPB CAPAcitance WRITE property [CARD] [write-range] [UNIT integer] READ PHI [UNIT integer] COOR coordinate-manipulation-commandpdetail.doc
File: PDETAIL, Node: Top, Up: (chmdoc/perturb.doc), Next: Introduction Details about TSM Free Energy Calculations * Menu: * Introduction:: What will be covered. * Theory and Methodology:: General discussion. * Practice:: How to do it. File: PDETAIL, Node: Introduction, Up: Top, Next: Theory and Methodology, Previous: Top Introduction For a good overview of free energy simulation methods, the follow- ing references are suggested: M. Mezei and D. L. Beveridge, in Annals of the New York Academy of Sciences, chapter titled "Free Energy Simulations", 482 (1986) 1; T. P. Straatsma, PhD dissertation, "Free Energy Evaluation by Molecular Dynamics Simulations", University of Groningen, Netherlands (1987) and S. H. Fleischman and C. L. Brooks III, "Thermodynamics of Aqueous Solvation: Solution Properties of Alchohols and Alkanes", J. Chem. Phys., 87, (1987) p. 3029, D. J. Tobias and C. L. Brooks III, J. Chem. Phys., 89, (1988) 5115-5127, and D.J. Tobias, "The Formation and Stability of Protein Folding Initiation Structures", Ph.D. dissertation Carnegie Mellon University (1991). In the previous nodes we have generally referred to this area of molecular simulation as a "perturbation" theory. Actually, none of the techniques used are actually perturbation methods. The relationships used for computing the relative free energy differences are all exact in the statistical mechanical sense. The use of the term perturbation in this context arises from the fact that in the pre-number crunching supercomputer days, various series expansions were derived from these equations and were in fact perturbation theories. The name thermodynamicpert.doc
File: Pert, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Free Energy Perturbation Calculations The PERTurbe command allows the scaling of energy between PSFs for use in energy analysis, comparisons, slow growth free energy simulations, widowing free energy simulation, and for slow growth homology modelling. This is a rather flexible implementation of free energy perturbation that allows connectivity to change. Also, three energy restraint terms (harmonic, dihedral and NOE) and the SKIP command flags are subject to change which allows a flexible way in which to compute free energy differences between different conformations. This code in implemented in a non-intrusive manner and works with all minimizers and integrators. SHAKE can now be applied to bonds which are mutated as well; an appropriate constraint corrections is calculated automatically in these cases. * Menu: * Syntax:: Syntax of PERT Commands * Description:: Description of PERT Commands * Restrictions:: Restrictions in PERT Command usage * References:: References regarding Free Energy Perturbations * Examples:: A Sample Input Files * Constraints:: Special considerations regarding SHAKE File: Pert, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax of Free Energy Perturbation Commands [Syntax PERT] PERTurb [OFF] [INBFrq int nonbond-specs] [RESEt] atom-selection [INBFrq 0 ] The PERT OFF command disables the free energy routines and the current (lambda=1) PSF is used for subsequent commands. When OFF is not specified, this command saves the current PSF as the lambda=0 state. The atom-selection indicated which atoms have changed. This is to make the calculation run more efficiently. If only a small percent of the atoms have changed, this doubles the performance. The nonbond specs areperturb.doc
File: Perturb, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Perturbation: Thermodynamic Perturbation Calculations. * Menu: * Syntax:: Syntax of the set up of the perturbation command. * Description:: Description of the keywords and options for setting up the perturbation calculation. Includes an explanation of the reset command TSM CLEAr. * Post-processing:: How to process the perturbation output of the dynamics run. * Details: (chmdoc/pdetail.doc). How to run perturbation calculations. * Implementation: (chmdoc/pimplem.doc). How it is implemented. Programming details. * CFTI: (chmdoc/cfti.doc). Conformational Energy/Free Energy Calculation (Krzysztof Kuczera) File: Perturb, Node: Syntax, Up: Top, Next: Description, Previous: Top Syntax for the Perturbation Command [SYNTAX TSM] TSM Chemical Perturbation Parameters: 1. REACtant atom_selection_list | NONE 2. PRODuct atom_selection_list | NONE 3. LAMBda <real> [ POWEr <int> ]pimplem.doc
File: PIMPLEM, Node: Top, Up: (chmdoc/perturb.doc), Next: Description Implementation of the Thermodynamic Simulation Method * Menu: * Description:: How Chemical Perturbation works. * File Formats:: Output File Formats for Chemical Perturbation. * IC Implementation:: Implementation and File Formats for Internal Coordinate Perturbation File: PIMPLEM, Node: Description, Up: Top, Next: File Formats, Previous: Top How the Chemical Perturbation Energy Calculation Works For thermodynamic perturbation calculations the atoms making up the system described by the hybrid Hamiltonian, H(lambda), can be divided into four groups. 1) The environment part - all atoms that do not change during the perturbation. E.g., for ethanol -> propane the solvent and the terminal methyl group. 2) The reactant atoms - the atoms that are present at lambda = 0 and absent at lambda = 1. 3) The product atoms - the atoms that are absent at lambda = 0 and present at lambda = 1. 4) The COLO atoms - atoms that are present in both the reactant and product but change charge in going from one to the other. Certain basic premises underly our approach. Energy values are factored by lambda (or functions thereof), never the energy functions themselves. The standard energy routines are called unchanged and can be modified without requiring changes to the perturbation routines as long as the calling sequence remains the same. Potential energy terms are written to output during a trajectory and in the case of the window method trajectories can be combined. Futhermore any lambda -> lambda'pressure.doc
File: Pressure, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Constant Pressure/Temperature (CPT) Dynamics Two types of constant pressure/temperature dynamics are available in CHARMM. The weak coupling method for temperature and pressure control described in the paper by Berendsen et al. (JCP 81(8) p3684 1984) was the first constant pressure and temperature algortihm implemented in CHARMM. Extended system constant pressure and temperature algorithms have now been implemented based on the work of Andersen (JCP 72(4) p2384 1980), Nose & Klein (Mol Physics 50(5) p1055 1983), Hoover (Phys. Review A 31(3) p1695 1985). Additionally, a variant on the extended system method which treats the control variables by means of a Langevin equation is available (Feller, Zhang, Pastor & Brooks, JCP, 103, 4613 (1995)). Shape matrix propagation and coordinates scaling for triclinic unit cell is done according to D. Brown and J.H.R. Clarke in Computer Physics Comm. 62 (1991) 360-369. A constant surface tension algorithm is included which is useful for studying interfacial systems where one wishes to allow the area to change dynamically during the simulation. The dynamical equations and statistical ensemble are discussed in (Zhang, Feller, Brooks & Pastor, JCP, 103, 10252 (1995)). * Menu: * Syntax:: Syntax of the CPT dynamics command * Description:: Description of the keywords and options * Notes:: Other points to be noted * Examples:: Isotropic and interfacial systems; constant tensor * Pressure:: The pressure command File: Pressure, Node: Syntax, Up: Top, Next: Description, Previous: Top [Syntax DYNAmics CPT] DYNAmics CPT ... cpt-spec cpt-spec::= [ pressure-spec ] [ temperature-spec ] [ surface-tension-spec ] pressure-spec::= PCONST {[PINTernal]} {BEREndsen berensen-spec} ref-pressure-specqmmm.doc
File: qmmm, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Combined Quantum and Molecular Mechanical Hamiltonian A combined quantum (QM) and molecular (MM) mechanical potential allows for the study of condensed phase chemical reactions, reactive intermediates, and excited state isomerizations. This is necessary since standard MM force fields are parameterized with experimental data on the potential energy surface which may be far removed from the region of interest, or have the wrong analytical form. A full decription of the theory and application is given in J. Computational Chemistry (1990) 6, 700. The effective Hamiltonian, Heff, describes the energy and forces on each atom. It is treated as a sum of four terms, Hqm, Hmm, Hqm/mm, and Hbrdy. Hqm Describes the quantum mechanical particles. The two semi- empirical methods available are AM1 and MNDO. Both treat hydrogen, first row elements plus silicon, phosphorus, sulfur, and the halogens. MNDO has additional parameters for aluminium, phosphorus, chromium, germanium, tin, mercury, and lead. Full details concerning these theoretical methods can be found in Dewar's original papers, JACS (1985) 107, 3902, JACS (1977) 99, 4899, Theoret. Chim. Acta. (1977) 46, 89. Hmm The molecular mechanical Hamiltonian is independent of the coordinates of the electrons and nuclei of the QM atoms. CHARMM22 is used to treat atoms in this region. Hqm/mm The combined Hamiltonian describes how QM and MM atoms interact. This is composed of two electrostatic and one van der Waals terms. Each MM atom interacts with both the electrons and nuclei of the QM atoms (therefore two terms). The van der Waals term is necessary since some MM atoms possess no charge and would consequently be invisible to the QM atoms, and in other cases often provide the only difference in the interaction (Cl vs. Br).replica.doc
File: Replica, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Replica: Commands which deal with replication of the molecular system: Replica. # <caves>-Aug-18-1993 (Leo Caves) Initial release. # REPLICA/PATH method added by B. Brooks March 1994. # Feynmann Path Integral Methods added by B. Roux, K. Hinsen and Marc Souaille, June 1997. The commands described in this node are associated with the replication of regions of the PSF, see *note gener:(chmdoc/struct.doc)Generate. A facility for replication of regions of the PSF has been implemented to support a class of methods which seek to improve the sampling of a (usually small) region of the molecular system, by selective replication. Such methods include LES (Locally Enhanced Sampling [Elber and Karplus 1990, J. Amer. Chem. Soc. 112, 9161-9175]) and MCSS (Multiple Copy Simultaneous Search [Miranker and Karplus 1991, Proteins 11, 29-34]). * Menu: * Syntax:: Syntax of the replication commands * Usage:: Description of command usage * Implementation:: A brief description of the anatomy of replication * Restrictions:: Restrictions on usage * Examples:: Supplementary examples of the use of REPLica * Path:: Replica Path Method * Pathint:: Path Integral Calculation using REPLica File: Replica, Node: Syntax, Up: Top, Next: Usage, Previous: Top Syntax of PSF Replication commands [SYNTAX: REPLication commands] REPLica { [segid] [NREPlica integer] [SETUP] [atom-selection] [COMP] } { RESEt } segid:== Basename for replica segment identifiers. atom-selection:== (see *note select:(chmdoc/select.doc).) { OFF } RPATh { [KRMS real] [KANGle real] [COSMax real] [MASS] [WEIGht] other-spec} other-spac:== [ KMIN real RMIN real ]rism.doc
File: RISM, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax RISM (Reference Interaction Site Model) module ------------------------------------------------ The RISM module allows the user to calculate the site-site radial distribution functions g(r) and pair correlation functions c(r) for a multi-component molecular liquid. These functions can then be used to determine quantities such as the potential of mean force or the cavity interaction term between two solute molecules into a solvent, and the excess chemical potential of solvation of a solute into a solvent. The change in the solvent g(r) upon solvation can be determined and this allows for the decomposition of the excess chemical potential into the energy and entropy of solvation. The code was written as an independent program by Benoit Roux in 1988. Some routines were added and it was adapted for CHARMM by Georgios Archontis in 1992. The help and advice of Hsiang Ai Yu is greatfully ackgnowledged. * Menu * Syntax:: Syntax of the RISM commands * Commands:: Explanation of the commands * Theory:: A brief introduction to the RISM theory * References:: Useful references * Examples:: Input files File: RISM, Node: Syntax, Up: Top, Next: Commands, Previous: Top Syntax for RISM calculation --------------------------- Invoke of the RISM command in the main charmm input file calls the subroutine RISM() (in rism.src). Once control has been transferred to this subroutine the subsequent commands are interpreted using a parser similar to the CHARMMrtop.doc
File: Rtop, Node: Top, Up: (chmdoc/commands.doc), Previous: (chmdoc/usage.doc)Standard files, Next: Overview Residue Topology File By Alexander D. MacKerell Jr., August 1999 This section of the documentation describes the contents of the topology file and a listing of the current topology files available to the users. CHARMM topology files contain the information necessary to describe bond connectivity, angle, dihedral angle and improper dihedral angle content, charge distribution, hydrogen-bond donors and acceptors and internal coordinate information. Thess data are required by CHARMM in order to determine energies, perform energy minimizations and molecular dynamics simulations as well as perform other various structural manipulations. Documentation concerning implementation of a topology file in order to build a structure is contained in STRUCT.DOC. * Menu: * Overview:: Overview of CHARMM Topology File * RTFDATA:: Description of Topology Files available for general use File: Rtop, Node: Overview, Up: Top, Next: RTFDATA, Previous: Top Overview of CHARMM Topology File An example of a topology file is given below followed by a description of the content of the various sections. Also see IO.DOC for information on the individual keywords. (A) * CHARMM example topology file * (B) 19 1 (C) MASS 1 H 1.00800 H MASS 2 O 15.99900 O (D) DECL -C DECL -O DECL +N DECL +H DECL +CAsbound.doc
File: Sbound, Node: Top, Up: (chmdoc/commands.doc), Previous: (chmdoc/cons.doc), Next: Syntax Method and implementation of deformable boundary forces The use of deformable boundary forces is in studying small localized regions of solvent, say around an active site. The boundary forces are applied to the atoms in the solvent and serve to contain the reaction zone. Generally the boundary forces are computed from the deformable boundary method of C. L. Brooks III and M. Karplus, J. Chem. Phys., 79, 6312(1983). Following generation one must; i) Generate the corresponding boundary potential ii) Read the tabulated boundary potential into CHARMM iii) Set-up the mapping CHARMM uses to connect table entries with boundary constrained atoms Steps ii) and iii) ** MUST ** be done everytime the boundary forces are to be used. For example, during the initial stages of a dynamics simulation and at all subsequent restarts. The syntax for generating the potential and reading and setting up the table structure is given in the following mode. * Menu: * Syntax:: Syntax for all the SBOUnd commands * Files: (chmdoc/support.doc)Boundary. Deformable boundary potential files File: Sbound, Node: Syntax, Up: Top, Previous: Top, Next: (chmdoc/support.doc)Boundary > SBOUnd POTEntial INPUt <integer> OUTPut <integer> Integrates forces to get potential and generates cubic spline approximation of the potential. > SBOUnd SET XREF <real> YREF <real> ZREF <real> ASSIgn <table number> <selection-syntax> Solvent boundary routine to set boundary geometry and specify the atoms referring to the tables. Note the assign must be repeated for each table entry. > SBOUnd READ UNIT <integer> This routine reads in the boundary potential splinesscalar.doc
File: Scalar, Node: Top, Up: (chmdoc/commands.doc) SCALar : commands to manipulate scalar atom properties [SYNTAX SCALar] SCALar keyname { } [atom-selection] { = keyname } ! A = B { COPY keyname } ! A = B { SUM keyname } ! A = A + B { PROD keyname } ! A = A * B { SET <real> } ! A = <real> { ADD <real> } ! A = <real> + A { MULT <real> } ! A = <real> * A { DIVI <real> } ! A = A / <real> { SIGN } ! A = sign ( A ) { INTEger } ! A = int ( A ) { RECIprocal } ! A = 1/ A { LOG } ! A = ln ( A ) { EXP } ! A = exp ( A ) { ABS } ! A = ABS ( A ) { NORM } ! A = A / 2-norm(A) { MIN <real> } ! A = MIN (A,<real>) { MAX <real> } ! A = MAX(A,<real>) { POWEr <real> } ! A = A ** <real> { POW2r } ! A = A * A { IPOW <real> } ! A = A ** int(<real>), OK for neg A { SQRT } ! A = SQRT(A) { RANDom } ! A = random { HBCOunt } ! A = #of hbonds { SHOW [SORT] } { STATistics weight_opt } { STORe store_number } ! S(i) = A(i) { RECAll store_number } ! A(i) = S(i) { +STOre store_number } ! S(i) = S(i) + A(i)select.doc
File: Select, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax ATOM SELECTION Atom selection is used for many commands within CHARMM. Its existance is one of the main factors in the versatility of CHARMM. * Menu: * Syntax:: Syntax of the sequential selection * Double:: Double atom selections * Function:: Descriptions of the various sequential options File: Select, Node: Syntax, Up: Top, Next: Double, Previous: Top Recursive Atom Selection Syntax [SYNTAX SELEction] .... SELEction <factor> [SHOW] END .... Listed in priority order (low to high) (operators not separated by a blank line are processed sequentially) <factor>:== <factor> .OR. <factor> <factor> .AND. <factor> <factor> .AROUND. <real> <factor> .SUBSET. <int*> <factor> .SUBSET. <int1> : <int2> .NOT. <factor> .BONDED. <factor> .BYRES. <factor> .BYGROUP. <factor> ( <factor> ) <token> <keyname> <token>::= SEGId <segid>* SEGId <segid1> : <segid2> ISEG <segnum1> : <segnum2> RESId <resid>* RESId <resid1> : <resid2> IRES <resnum1> : <resnum2>shapes.doc
Shape Descriptors A CHARMM section to deal with shapes and charge distributions for small molecules. By Bernard R. Brooks and Yuhong Zhang - NIH Overview A shape descriptor facility has been developed with several goals in mind; - Best fit two or more molecules based on shape. - Docking small molecules into an active site. - Optimize the conformation of a molecule to achieve a particular shape. - Optimize the conformation of two molecules so that they give the same shape. - Generate descriptors of a molecule for QSAR applications. - To provide a simple graphic representation of a molecule. It also provides the capability for: - Rigid body minimizations - Rigid body dynamics - Rigid and flexible docking - Structural analysis of miscellaneous properties (e.g. hydrophobic moments) - Searching a trajectory for frames with a given property/shape - High volume screening when coupled with a structural database This is achieved by representing a molecule's shape and charge distribution (and other properties) as series of a polynomic expansion in cartesian space. A new data structure, Shape Descriptors, has been created. The following commands and command features have been added to CHARMM to manipulate and utilize this data structure; Syntax: -------------------------------------------------------------------------------- Commands defining the shape descriptor tables: SHAPe { CLEAr [PROPerties] } - clear the descriptor datastruct.doc
File: Struct, Node: Top, Up: (chmdoc/commands.doc), Next: Generate Generation and Manipulation of the Structure (PSF) The commands described in this node are used to construct and manipulate the PSF, the central data structure in CHARMM (see PSF.FCM). The PSF holds lists giving every bond, bond angle, torsion angle, and improper torsion angle as well as information needed to generate the hydrogen bonds and the non-bonded list. It is essential for the calculation of the energy of the system. A separate data structure deals with symmetric images of the atoms. See *note Images: (chmdoc/images.doc). There is an order with which commands to generate and manipulate the PSF must be given. First, segments in the PSF must be generated one at a time. Prior to generating any segments, one must first have read a residue topology file, see *note read:(chmdoc/io.doc)Read. To generate one segment, one must first read in a sequence using the READ command, see *note seq:(chmdoc/io.doc)Sequence. Then, the GENERATE command must be given. Once a segment is generated, it may be manipulated. This can be done in a very general way using the patch command. The patch command allows, for instance, the addition of disulfide bridges, changing the protonation state of a titratible residue or to make a histidine heme crosslink. The PSF can be saved with the "WRITE PSF" command. A PSF may be read with the "READ PSF" command. The "READ PSF" command has an "APPEnd" option that allows the merging of individual PSF files. In addition, the "DELETE" command allows the deletetion of atoms and all references to the deleted atoms. * Menu: * Generate:: Generating a segment * Nbx:: Nonbond exclusion lists * Patch:: Multi purpose patch command to modify the PSF * Autogen:: Autogenerate angles and/or dihedrals after patchessubst.doc
File: SUBST, Node: Top, Up: (chmdoc/commands.doc), Next: Substition:(chmdoc/energy.doc), Previous: (chmdoc/commands.doc) Command Line Substitution Parameters The following are substitution parameters available within CHARMM; --------------------------------------------------------------------- General: 'PI ' - Pi, 3.141592653589793 'KBLZ' - The Boltzmann factor (0.001987191) 'CCELEC' - 1/(4 PI epsilon) in AKMA units (332.0716) 'SPEEDL' - Speed of light 'CNVFRQ' - Conversion from root(Kcals/mol/AMU) to frequencies in CM-1. 'TIMFAC' - Conversion from AKMA time to picoseconds --------------------------------------------------------------------- Control and system variables: 'BOMLEV' - The error termination level (-5 to 5) 'WRNLEV' - The warning print level (-5 to 10) 'PRNLEV' - The standard print level (-1 to 15) 'IOLEV' - The I/O level (-1 to 1) 'IOSTAT' - The status of most recent OPEN command (-1=failed,1=OK) 'TIMER' - 'FASTER' - 'LFAST' - 'OLMACH' - 'OUTU' - 'FLUSH' - 'FNBL' - 'NBFACT' - 'LMACH' - 'MYNODE' - Current node number (0 to NUMNODE-1) 'NUMNODE' - The number of nodes (distributed memory) 'NCPU' - The number of CPUs (shared memory use) 'SYSSTAT' - ---------------------------------------------------------------------support.doc
File: Support, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/usage.doc), Next: (chmdoc/testcase.doc) Support Programs and Data Files This section describes supplimentary programs and data files included in the CHARMM 22.0.b package. * Menu: * Boundary:: Deformable boundary potential files * IMTRAN:: Image transformation files File: Support, Node: Boundary, Up: Top, Previous: Top, Next: IMTRAN Deformable Boundary Potential Files A deformable boundary potential (DBP) file is required to run the stoichastic boundary molecular dynamics (SBMD) simulatiuon. Only spherical DBP's are included in the current release. In the future release, cylindrical boundaries and plane shape boundaries will be incorporated and the DBP generation routine will also be available through CHARMM. ~/charmm/support/bpot (or [...CHARMM.SUPPORT.BPOT] on VMS machines) contains DBP files for the TIP3P water in a spherical simulation zone with 8 to 25 angstrom effective radius. These DBP files are generated by using Charlie Brooks' MFFGEN1 program and the CHARMM SBOUND command. The effective radius is set to the Langevin and reservior region boundary (the reaction zone radius). Then, the boundary radius used in the DBP generating program (e.g., MFFGEN1.EXE on HUCHE1.HARVARD.EDU) should be larger than the reaction zone radius by the water oxygen van der Waals radius. The reaction zone radius plus 1.7682 angstrom (the TIP3P water oxygen vdW radius) is used to generate the DBP for a given effective radius sphere. The nonbonded cutoff of 7.5 angstrom is used in the DBP generation procesure. Those DBP files can be used in simulations with different nonbonded cutoff distances. See *note Sbound: (chmdoc/sbound.doc), for details on the SBOUND command. File: Support, Node: IMTRAN, Up: Top, Previous: Boundary, Next: Toptest.doc
File: Test, Node: Top, Up: (chmdoc/commands.doc) Test commands: Commands to test various conditions in CHARMM [SYNTAX TEST] Syntax of the TEST commands: TEST FIRSt [TOL real] [STEP real] [UNIT int] [MASS int] [atom-selection] (0.005) (0.0001) (6) (0) [ CRYStal [ HOMOgeneous ] ] TEST SECOnd [TOL real] [STEP real] [UNIT int] (0.005) (0.0001) (OUTU (6)) TEST COORdinates [COMP] TEST CONNectvity [SUBSet atom-selection] [COMMon atom-selection] [PRINt] TEST PSF TEST PARAmeter TRIGonometry { DIHEdral } { CDIHedral } { VDIHedral } { IMPRoper } TEST HEAP TEST STACk GETHeap integer TEST INITialization RESET TEST NOCOmmunication { READ UNIT int STEP int MEMO int } { WRITE UNIT int STEP int MEMO int } { CLOSE } TEST STAMp LEVEl int The TEST FIRSt command, tests the first derivative of the energy by finite differences. It uses the GETE subroutine, so that before this command is invoked, the UPDAte command must be invoked. Since two energy evaluations are done for each degree of freedom, an atom selection should be used for large systems. The TOL keyword may be used to list only those terms which differ by more than a particular tolerance factor. The STEP keyword gives the finite difference steptestcase.doc
File: Testcase, Node: Top, Up: (chmdoc/charmm.doc), Previous: (chmdoc/support.doc), Next: (chmdoc/developer.doc) CHARMM Testcases The CHARMM test cases are designed to test features of CHARMM and some of error handling. Though the test cases are not designed as a tutorial and some used options and input parameters are not recommended, the test cases are a valuable learning tool in setting up input files for CHARMM. * Menu: * Overview:: Notes about testcases * Instruction:: How to run testcases * C20TEST:: Description of testcases in c20test * C22TEST:: Description of testcases in c22test * C23TEST:: Description of testcases in c23test * C24TEST:: Description of testcases in c24test * C25TEST:: Description of testcases in c25test * C26TEST:: Description of testcases in c26test * NBONDTEST:: Description of testcases in cnbondtest * MMFFTEST:: Description of testcases in cmmfftest * GRAFTEST:: GRAPHICS Testcases File: Testcase, Node: Overview, Up: Top, Previous: Top, Next: Instruction Notes about the Testcase Suite Testcases are reformed. All testcases before version 22 are collected in ~/cnnXm/test/c20test and new tests are written while we develop CHARMM. The new testcases are gathered in ~cnnXm/test/c22test, c23test, ... Note the following. (1) In the new testcase suite, we use formatted I/O for topology/parameter files in order for all testcases to run independently each other. (2) We make testcases self-contained whenever possible. If external data files are required to run the test, they are in ~/cnnXm/test/data. (3) CHARMM command parameter 0 and 9 are reserved to point directories for data and scratch files. These are defined in the stream file ~/cnnXm/test/datadir.def. The defaulttravel.doc
Documentation for TRAVEL ver. 3.10 in CHARMM. By Stefan Fischer. June 1-1996. File: Travel, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax ********************************************************* * TRAVel (Trajectory Refinement Algorithms) Command * ********************************************************* This module offers access to the CPR (Conjugate Peak Refinement) algorithm for finding reaction-coordinates (described in S.Fischer and M.Karplus, Chem. Phys. Letters vol.194, p.252, 1992), as well as to several other tools for refining and analyzing a reaction-path. * Menu: * Syntax:: Syntax of the TRAVel command * MainCmd:: TRAVel main command and miscellaneous subcommands * TrajManip:: TRAVel TRAJectory subcommand (input/output/analysis) * CPRcmd:: TRAVel CPR subcommand description * SDPcmd:: TRAVel CROS and SDP subcommand description * SCMcmd:: TRAVel SCM subcommand description * Usage:: TRAVEL Usage Note File: Travel, Node: Syntax, Up: Top, Previous: Top, Next: MainCmd ************************************* * Syntax for the TRAVEL Command * ************************************* Keywords in [...] are optional. Default values are given in (...). Choose one from list : {...|...|...} Main command (entering and leaving the TRAVEL module) : ------------------------------------------------------- TRAVel [MAXPoints int (100) ] [ { XAXI | YAXI | ZAXI } [ ROTAtion ] ] [ SCALe [{ COMP | WMAIn }] ] { END | QUIT } Subcommands (within TRAVEL module) : ------------------------------------ [VERBose int (2) ] [DISPlay int (80)]umbrel.doc
Charmm Element doc/umbrel.doc $Revision: 1.1 $ File: Umbrel, Node: Top, Up: (chmdoc/commands.doc), Next: RXNCOR Umbrella Sampling along a Reaction Coordinate --------------------------------------------- By J. Kottalam, December 1990 This module of charmm is used for defining a reaction coordinate for any molecule based on its structure and impose an umbrella potential along that reaction coordinate (i.e., to run activated dynamics along this coordinate) in order to trace out the free energy profile during the structural change along the coordinate. * Menu: * RXNCOR:: Specifying a reaction coordinate in CHARMM * Dynamics:: Running dynamics under an umbrella potential * Statistics:: Extracting results from umbrella dynamics * Results:: Interpreting and using the results File: Umbrel, Node: RXNCOR, Up: Top, Next: Dynamics, Previous: Top I. Specifying a reaction coordinate in CHARMM A reaction coordinate is either a distance or an angle. In some cases it can be a linear combination of distances or angles. For example, the interconversion between the chair and boat forms of cyclohexane can be described in terms of three rotation angles. These angles rotate carbons 2, 4 and 6 respectively about the plane of carbons 1, 3 and 5. In some other cases the reaction coordinate can be a ratio of two distances. In proton transfer between atoms A and B the ratio of A - proton distance to the A - B distance is a good measure of the extent of reaction. A distance can be between two points or the perpendicular distance of a point from a plane or a line. An angle can be between two (intersecting or non-intersecting) lines and so on. Planes and lines are ultimately defined in terms of points and points can be defined as the centres of geometry (or mass)usage.doc
File: Usage, Node: Top, Up: (chmdoc/charmm.doc), previous: (chmdoc/install.doc), Next: (chmdoc/support.doc) How to use CHARMM The user of CHARMM controls its execution by executing commands sequentially from a command file or interactivly. In general the ordering of commands is limited only by the data required by the command. For example, the energy cannot be calculated unless the arrays holding the coordinates, the parameters, etc., have already been filled. This section deals with overall usage, as opposed to the detailed description of any given command. This is a good place to start when first learning CHARMM. * Menu: * Meta-Syntax:: Describing the Syntax of Commands * Command Syntax:: Rules for composing command input files. * Run Control:: Ways to modify control flow and stream switching. * I/O Units:: Correspondence between files and unit numbers used by CHARMM. * AKMA:: Units of Measurement used in CHARMM * Data Structures:: Data Structures used by CHARMM * Standard Files:: Descriptions of parameters, topologies, and coordinates available. * Examples:: Sample runs * Interface:: How to make your own private version of CHARMM * Syntactic Glossary:: Glossary of syntactic terms * Glossary:: Glossary of non-syntactic terms. File: Usage, Node: Meta-Syntax, Up: Top, Next: Command Syntax, Previous: Top Rules for Describing the Syntax (The Meta-Syntax) The syntax of commands is described using the following rules: Capitalized words are keywords that must be specified as is. However, if the word is partially capitalized, it may be abbreviated to the capitalized part. Lower case words are to be replaced by a corresponding data entry. The symbol "::=" means "has the following syntactic form:". Anything enclosed in square brackets, "[]", is optional. If severalvibran.doc
File: Vibran, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Vibration Analysis The vibrational analysis section of CHARMM has been designed to be a general purpose normal mode generation and analysis facility. Also included is an extensive set of vector analysis and comparison features. Support programs such as the iterative diagonalization program, or the restartable large matrix diagonalization program are compatable with this facility. Also included are routine to generate trajectories which can be used for examining modes on the picture system. In order to process commands with the vibrational analysis routines, The energy terms must all be defined, and the structure must be determined (see *note Needs: (chmdoc/energy.doc)Needs.). At present, SHAKE and images (see *note Images: (chmdoc/images.doc).) are not supported. Systems with atoms fixed by the CONStraint FIX command can be treated by using the REDU FIX option. Within the vibrational analysis command mode, all miscellaneous (MISCOM), coordinate manipulation (CORMAN), and internal coordinate (IC) commands are allowed. Keywords used to define Hydrogen bonds and nonbonded interactions may be included in the command that invokes VIBRAN. * Menu: * Syntax:: Syntax of the VIBRan command and all commands * Normal modes:: Description of normal modes * I/O:: Description of the read and write commands. * Diagonalization:: Description of the diagonalization command. * Quasiharmonics:: Description of the quasiharmonics command. * Reduce:: Reduced basis normal mode analysis * Dimb:: Iterative diagonalization (DIMB). * Explore:: Command to explore the energy hypersurface * Fluctuations:: Description of the fluctuation command. * Princ-Axis-Flucts:: Description of the PAFL command.
CHARMM Documentation / Rick_Venable@nih.gov