namd Overview

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. For more information visit NAMD website.

Support

Usage

NAMD is available on Titan as a module. 
module load namd
which namd2
Will add namd2 (executable) to your PATH. Please set the following environment variables in you job submission script: 
setenv MPICH_PTL_SEND_CREDITS -1
setenv MPICH_MAX_SHORT_MSG_SIZE 8000
setenv MPICH_PTL_UNEX_EVENTS 80000
setenv MPICH_UNEX_BUFFER_SIZE 100M
Builds

TITAN

  • namd@2.12%gcc@4.9.3
  • namd@2.12%gcc@4.9.3