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Molecular Dynamics Productivity Environment

Molecular Dynamics productivity environment includes a set of tools which are need for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the LinkSCEEM-2 communities and set an action plan.

BC Policy: LS2_11-95
Date of Policy: 1st January 2012
First Update: 16th December 2011
Second Update: 30th January 2012

The main objective of this policy is to provide the following common productivity environment across any LinkSCEEM-2 resources:

Name Prefered version(s) Compliance level Reference
GROMACS v4.5.5 MUST http://www.gromacs.org/
CHARMM c36b1 MUST http://www.charmm.org/
NAMD v2.8 MUST http://www.ks.uiuc.edu/Research/namd/
VMD v1.9 MUST http://www.ks.uiuc.edu/Research/vmd/
DL_POLY v4.02 MUST http://www.ccp5.ac.uk/DL_POLY/
LAMMPS v1May2010 MUST http://lammps.sandia.gov/
CPMD v3.15.1 MUST http://www.cpmd.org/
CP2K latest MUST http://www.cp2k.org/
NWCHEM v6.1 MUST http://www.nwchem-sw.org/
AMBER v11 SHOULD http://ambermd.org/
XMakemol v5.16 SHOULD http://www.nongnu.org/xmakemol/

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 technical representative & LS2 user-support.
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