Software used on LoBoS
Researchers who use LoBoS require a wide array of software to conduct
molecular modeling and simulations, as well as support software to keep
Molecular Modeling Software
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.
A piece of commercial software that performs quantum chemistry calculations is
Q-Chem. Q-Chem uses efficient techniques
to parallelize methods such as Hartree-Fock and DFT single-point energies, geometry
optimizations, and frequency calculations. Q-Chem combines these advanced techniques
into a single package for use in ab initio computations. Q-Chem is also
capable of performing QM/MM calculations via a CHARMM QM/MM interface.
Another ab initio package we have available
Both software packages provide means of performing QM/MM calculations via
a CHARMM QM/MM interface.
Another piece of commercial software that performs quantum calculations is
which also performs ab initio analyses of complex molecular systems. It contains
many advanced features such as the ONIOM method of analyzing the electribuc
structure of large molecules and the Polarizable Continuum Model for studying
molecules in solution.
Another molecular dynamics package we use is
AMBER (Assisted Model Building with Energy Refinement). It is designed with
particular emphasis on studying the dynamics ofbiomolecules. AMBER consists of a
variety of tools such as SANDER, which performs basic molecular dynamics and PTRAJ,
which analyzes the coordinate files produced by the simulation.
GROMACS is a free (GPL) and
versatile package for performing classical molecular dynamics simulations. It conmes with a wide range of tools
for analysis, and has been parallelized using MPI.
NAMD is 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.
VMD is 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).
Compilers and Parallel Execution Tools
- Most of our compiling is done with the open-source
GNU Compiler Collection. The versions of MPICH that we currently use
are compiled with versions 4.1.1 and 4.2.2 of gcc.
- OpenMPI is a portable
implementation of the MPI parallel computing standard. The software was
developed by a consortium of commercial and academic institutions. We currently use the 1.5 series.
The parallel CHARMM jobs we run on LoBoS use OpenMPI to handle their
Administrative and Monitoring Software
- The LoBoS job scheduler is the
TORQUE Resource Manager distributed by
Adaptive Computing, Inc. We currently use version 2.5.7. TORQUE is an improvement over
OpenPBS and in tests it has been able
to scale to managing over one thousand jobs simulataneously.
- We've 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.