Researchers who use LoBoS require a wide array of software to conduct molecular modeling and simulations, as well as support software to keep everything running.

Molecular Dynamics

  • CHARMM. The primary modeling tool used on the cluster is the CHARMM (Chemistry at HARvard Molecular Mechanics) software package. Dr. Bernard Brooks, the head of the LCB, is one of the primary developers of CHARMM. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the package.
  • AMBER. (Assisted Model Building with Energy Refinement) is designed with particular emphasis on studying the dynamics of biomolecules. AMBER consists of both freely-available tools for molecular dynamics (MD) simulation and analysis via AmberTools (including the MD engine SANDER and the parallelized MD analysis program CPPTRAJ, which can process data from AMBER, CHARMM, Gromacs, and NAMD), as well as the highly-optimized and GPU-enabled MD engine PMEMD.
  • GROMACS. A versatile package for performing classical molecular dynamics simulations. It comes with a wide range of tools for analysis, and has been parallelized using MPI.
  • NAMD. A parallel molecular dynamics program. Its main feature is its extreme scalability. It can be run on hundreds of processors to efficiently characterize the dynamics of very large systems. It is compatible with input files of other software such as CHARMM, AMBER, and X-PLOR.
  • Tinker. Molecular modeling software that is being used in the laboratory. It is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
  • OpenMM. A freely-available toolkit for molecular simulation. Can be used either as a stand-alone application for running simulations, or as a library that can be called from other codes. Both CHARMM and AMBER can make use of OpenMM functionality.

Quantum Mechanics

  • GAMESS. Another ab initio package we have available is GAMESS-US. This software package provides means of performing QM/MM calculations via a CHARMM QM/MM interface.
  • Gaussian. Another piece of commercial software that performs quantum calculations is Gaussian, which also performs ab initio analyses of complex molecular systems. It contains many advanced features such as the ONIOM method of analyzing the electronic structure of large molecules and the Polarizable Continuum Model for studying molecules in solution.
  • Psi4. An open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.

Molecular Visualization

  • VMD. A multiplatform molecular visualization program. It supports many different coordinate and structure file formats, including those used by CHARMM, PQR, and AMBER. It also is able to read GAMESS log files. We use it to create beautifully rendered images of the molecular systems which we study (some of which can be found on this Web site).
  • PyMOL. A flexible molecular graphics and modelling package which can be also used to generate animated sequences.
  • Molden. A visualization program of molecular and electronic structure.

Compilers and Parallel Execution Tools

  • GNU Compiler Collection. We used the open-source compilers for multiple applications.
  • Intel Compiler Collection. Most of our compiling is done with these compilers.
  • PGI Compilers. Contains Fortran 95, Fortran 90, Fortran 77, C, and C++ compilers
  • OpenMPI. A portable implementation of the MPI parallel computing standard. The software was developed by a consortium of commercial and academic institutions.
  • MVAPICH. An open-source MPI software that is optimized to take advantage of the novel features and mechanisms of high-performance networking technologies such as the Infiniband interconnect.
  • Intel MPI. An MPI library that focuses on making applications perform better on Intel architecture-based clusters.

Administrative and Monitoring Software

  • SLURM Workload Manager. An open source, fault-tolerant, and highly scalable cluster management and job scheduling system. This will eventually be used to manage the entire LoBoS cluster.
  • NAGIOS. We have found Nagios useful for general cluster monitoring and supervising important systems such as our RAID arrays. Nagios can automatically notify an administrator by e-mail when it detects a problem.