HPCBIOS_2012-95: Molecular Dynamics Productivity EnvironmentΒΆ


Molecular Dynamics productivity environment includes a set of tools which are needed for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.

  • BC Policy: HPCBIOS_2012-95
  • Date of Policy: 2012-12-15

The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:

Name Prefered version(s) Compliance level Reference
GROMACS v4.5.5 or later MUST http://www.gromacs.org
CP2K 20111205 or latest MUST http://www.cp2k.org
CHARMM c37b2 SHOULD http://www.charmm.org
NAMD v2.8 MUST http://www.ks.uiuc.edu/Research/namd
VMD v1.9 SHOULD http://www.ks.uiuc.edu/Research/vmd
DL_POLY v4.02 SHOULD http://www.ccp5.ac.uk/DL_POLY
LAMMPS v1Feb2014 or later SHOULD http://lammps.sandia.gov
CPMD v3.15.1 SHOULD http://www.cpmd.org
NWCHEM v6.1 SHOULD http://www.nwchem-sw.org
XMakemol v5.16 SHOULD http://www.nongnu.org/xmakemol
TINKER v6.0.08 SHOULD http://dasher.wustl.edu/tinker/
HOOMD-blue v0.10.0 SHOULD http://codeblue.umich.edu/hoomd-blue/
AMBER v11 SHOULD http://ambermd.org

This productivity environment will be supplemented with other related productivity tools as they become available on allocated systems.

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.