Center for Computational Molecular Science and Technology Georgia Institute of Technology Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry

CCMST Weekly News, February 17 2012

February 17, 2012 3:50 pm EST

1. Announcements
2. Tip of the Week

ANNOUNCEMENTS

AACP Seminar

February 20, 2012 8:00 PM – 9:00 PM
MoSE G011
Prof. Michael Heaven, Emory University
Spectroscopic Studies of Prototype Actinide Compounds (and closely related species)

Cherry Emerson Lecture

February 23, 2012 4:00 PM – 5:00 PM
MoSE G011
Dr. Stephen Padgette, Vice President of Biotechnology, Monsanto
Innovation in Agriculture: Biotechnology, Genetics, Genomics & Beyond

TIP OF THE WEEK

By Massimo

Amber

Amber version 11 and AmberTools version 1.5 are now available on egate and fgate. In addition to the single processor version, parallel jobs are available for sander.MPI, sander.LES.MPI, sander.RISM.MPI and pmemd.MPI. Here are sample scripts for running sander:

  • Single processor job
    #!/bin/bash
    #PBS -N cytosine
    #PBS -j oe
    #PBS -l pmem=400mb
    #PBS -l walltime=01:00:00:00

    #
    # environment for Intel compiler version 11
    #

    export PATH=opt/intel/Compiler/11.1/075/bin/intel64:$PATH
    export LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/075/lib/intel64:/opt/intel/Compiler/11.1/075/mkl/lib/em64t:$LD_LIBRARY_PATH

    #
    # set Amber environment
    #

    export AMBERHOME=/share/apps/amber11

    #
    # run job
    #

    cd ${PBS_O_WORKDIR}

    ${AMBERHOME}/bin/sander -O -i in.md -c crd.md.23 -o cytosine.out
  • parallel job
    #!/bin/bash
    #PBS -N cytosine
    #PBS -j oe
    #PBS -l nodes=4:ppn=1
    #PBS -l pmem=400mb
    #PBS -l walltime=01:00:00:00

    #
    # environment for Intel compiler version 11 and openmpi
    #

    export PATH=opt/intel/Compiler/11.1/075/bin/intel64:$PATH
    export LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/075/lib/intel64:/opt/intel/Compiler/11.1/075/mkl/lib/em64t:$LD_LIBRARY_PATH
    export PATH=/share/apps/openmpi-1.4.4/intel-11/bin:$PATH
    export LD_LIBRARY_PATH=/share/apps/openmpi-1.4.4/intel-11/lib:$LD_LIBRARY_PATH


    #
    # set Amber environment
    #

    export AMBERHOME=/share/apps/amber11

    #
    # display number of processors and hosts file.
    #

    NP=`cat ${PBS_NODEFILE} | wc -l`
    echo "number of processes = ${NP}"
    cat ${PBS_NODEFILE}

    #
    # run job
    #

    cd ${PBS_O_WORKDIR}

    mpirun ${AMBERHOME}/bin/sander.MPI -O -i in.md -c crd.md.23 -o cytosine.out

For further info, please refer to the CCMST wiki Amber  page.

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo (massimo.malagoli@chemistry.gatech.edu) for inclusion in the Tip of the Week section.