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 everything running.

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 GAMESS-US and GAMESS-UK. 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 Gaussian, 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 MPI communication.

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.