Amber

General Information

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PythonMPT
ambermd.org12python/2.7.2mpt/2.06

Amber is a program suite for molecular dynamics simulations.

Usage on Vilje

Load the following modules to use amber on Vilje:

$ module load mpt/2.06 python/2.7.2 amber/12

All below under contruction …

Sample Job Script

#!/bin/bash
###################################################
#
#  Amber job
#
###################################################
#
#PBS -N test
#PBS -A nn1234k
#PBS -l select=2:ncpus=32:mpiprocs=16
#PBS -l walltime=24:00:00
#
 
module load mpt/2.06
module load python/2.7.2
module load amber/12
 
case=$PBS_JOBNAME
 
cd $PBS_O_WORKDIR
 
# Create (if necessary) the working directory
w=/work/$PBS_O_LOGNAME/amber/$case
if [ ! -d $w ]; then mkdir -p $w; fi
 
# Copy inputfiles and move to working directory
cp $case.inp $w
cd $w
 
mpiexec_mpt amber $case.inp

Test case: Xyz…

This test case illustrate how to …

See the Amber Tutorials web page for a detailed description of this test case.

  1. Unpack the test case files$ tar zxf /sw/sdev/Modules/amber/test_case.tar.gz
  2. Replace nn1234k with your project account number in the amber.pbs job script, and submit the job to the queuing system$ qsub amber.pbs
  3. When the job has finished, check the output file and compare with the outputtest_case.out included in test case.

Further Information