Ada : NAMD

Introduction

NAMD is a classical molecular dynamics software. It is designed for high-performance simulations of large biomolecular systems.

Availability

The following versions are available :

  • 2.8
  • 2.9 (default)

The parallel MPI version is available on Ada.

Launching script

To know which different versions are installed:

module avail namd

To load a particular version:

module load namd/2.9

Here is an example of a launching script for a calculation executed in the WORKDIR :

job.ll
# @ job_name         = NAMD
# @ job_type         = parallel
# @ output           = $(job_name).$(jobid)
# @ error            = $(output)
# @ wall_clock_limit = 1:00:00
# @ total_tasks      = 64
# @ queue
 
### Module initialisation ###
module load namd/2.9
 
### Command echoes ###
set -x
 
### Run the calculation ###
poe namd2 apoa1.namd

Here is an example of a launching script for a calculation executed in the TMPDIR :

job.ll
# @ job_name         = NAMD
# @ job_type         = parallel
# @ output           = $(job_name).$(jobid)
# @ error            = $(output)
# @ wall_clock_limit = 1:00:00
# @ total_tasks      = 64
# @ queue
 
### Module initialisation ###
module load namd/2.9
 
### Command echoes ###
set -x
 
### Copy to the TMPDIR ###
cp ./* $TMPDIR
 
### Run the calculation ###
cd $TMPDIR
poe namd2 apoa1.namd
 
### Copy to the submission folder ###
cd -
cp $TMPDIR/* .

The following is an example of a script submission for a job called job.ll:

llsubmit job.ll

Documentation