[3646] in Software_Announce
NAMD installed on Athena
daemon@ATHENA.MIT.EDU (Alex T Prengel)
Wed Apr 13 20:10:23 2011
From: Alex T Prengel <alexp@MIT.EDU>
To: software-announce@mit.edu
Cc: alexp@mit.edu, vsls-team@mit.edu, cfyi@mit.edu
Date: Wed, 13 Apr 2011 20:10:16 -0400
I've installed NAMD on Athena (in the vmd lockers, as it's related to
that application). NAMD is a parallel molecular dynamics code based on
Charm++ parallel objects and designed for high-performance simulation of
large biomolecular systems. NAMD uses VMD for simulation setup and
trajectory analysis, but is also file-compatible with AMBER, CHARMM, and
X-PLOR. It can be used on Athena but with limited performance as current
Athena machines only have two processing cores, and don't have access to
parallel processing grids on the network. Command line invocation is
similar to this:
charmrun ++local <options> `athdir /mit/vmd`/namd2 <configfile>
but the application is complex and there are multiple options which are
likely to require reading the documentation and/or scripts that run
simple demos to master. You can get to these through:
http://web.mit.edu/vmd_v1.8.7/README.athena
Cheers,
Alex
