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NAMD (Application)

Introduction

NAMD (NAnoscale Molecular Dynamics) is a molecular dynamics simulation package developed at the University of Illinois at Urbana-Champaign. Based on Charm++ parallel objects, NAMD is noted for its parallel efficiency and is designed for high-performance simulation of large biomolecular systems. SHARCNET clusters and SMP systems have the mpi version installed therefore jobs must be submitted to the parallel queue as shown below. Scaling tests should always be performed to determine the optimal number of processors to be used on a given system prior to a long run.

Availability Table

Version Default Module Systems
2.10 True orca, wobbie
2.10 (gpu) True copper, monk, mosaic
2.11 True orca, wobbie
2.11 (gpu) True copper, monk, mosaic
2.8 True orca, wobbie
2.9 True orca, wobbie
2.9 (gpu) True copper, monk, mosaic

Documentation

https://www.sharcnet.ca/help/index.php/NAMD

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Change Log

o Oct 20, 2016 - Installed namd/intel1503-openmpi187std-cuda7518/2.11 on angel, copper and mosaic. Note that angel is only accessible from saw by doing: ssh ang1.angel
o Sep 16, 2016 - Installed namd/intel1503-openmpi187std-cuda7518/2.11 on monk.
o Jan 28, 2016 - Installed namd/2.8, namd/2.10, namd/2.11 on brown, saw, redfin, wobble.
o Jan 18, 2016 - Installed namd/2.10 and namd/2.11 on orca for testing.
o Oct 15, 2015 - Removed namd/gpu/2.9 from angel.
o Jun 25, 2014 - Reinstalled namd/2.8 on orca for temporary usage see tk23013.
o Apr 22, 2014 - Removed namd/2.8 from brown, goblin, guppy, hound, kraken, mako, orca, redfin and saw. Removed namd/gpu/2.8 from angel and monk.
o Mar 13, 2014 - Updated 2.9 on monk to include MPI and MPI-SMP versions.
o Oct 22, 2013 - Removed 2.7b1 from requin and 2.7, 2.7b3, 2.8b1 from guppy and mako.
o Feb 22, 2013 - Installed 2.9 non-gpu version on orca, saw and redfin.
o Apr 17, 2012 - Install gpu enabled namd 2.8 on monk (submit jobs to gpu queue only).
o Jun 03, 2011 – Installed namd/2.8 (2011-05-31) on angel, brown, goblin, guppy, hound, mako and orca. Note that namd2-mpi-cuda is not included in this build for angel. Removed all versions of namd from gulper (removal from kraken is pending).
o May 02, 2011 – Installed 2.8b1 providing namd2-mpi (and namd2-mpi-cuda for use on angel).
o Mar 09, 2011 - Installed Namd Version 2.7 (2010-10-15) built from source including binaries: namd2-mpi, namd2-mpi-cuda, namd2-mpi-cuda-patched and namd2-mpi-patched. Note that the namd2 link to namd2-mpi is no longer included in the bin sub-directory.
o May 02, 2011 – Installed 2.8b1 providing namd2-mpi (and namd2-mpi-cuda for use on angel).