Wednesday, 28 February 2007

amber on clustervision1

The amber 9.0 has been compiled on clustervision1 using Intel Fortran compiler and mpich2. It is located at /usr/local/bin/amber.
How to use?
First you need to set the environment variable AMBERHOME to /usr/local/bin/amber either by putting the following line in your .bashrc.
"export AMBERHOME=/usr/local/bin/amber"
or simply run this command for one-time use.
One simple Perl script for running parallel sander have been attached.

#!/usr/bin/perl
system("perl /usr/local/Cluster-Apps/environment-modules-3.1.6/init/perl");
system("export MPICH_PROCESS_GROUP=no");
$name="adxylp20";
$MYAPP="$AMBERHOME/exe/sander.MPI";
#$ -cwd
#$ -N adxylp202
#$ -v MPICH_HOME
#$ -pe mpich_mx 2
system("$ENV{MPICH_HOME}/bin/mpirun -np $ENV{NSLOTS} -machinefile $ENV{TMPDIR}/machines ${MYAPP} -O -i
${name}min.in -o ${name}min.out -c ${name}.crd -p ${name}.top -r ${name}min.rst -x ${name}min.mdcrd
-inf ${name}min.mdinf");

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