Amber

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"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.

Project website: http://ambermd.org/

Load SGE module

The following Modules files should be loaded for this package (the amber module will automatically load the openmpi module):

For Intel:

module load amber/amber-10-intel

Use the openmpi parallel environment in your job script (example for a 4 slot job)

#$ -pe openmpi 4

Use Amber on the Cheaha

Sample Job script for Amber

 Create a job submit script as shown below called 'amberSubmit', make sure to edit the following parameters:

 * s_rt to an appropriate soft wall time limit
 * h_rt to the maximum wall time for your job
 * -N - job name
 * -M - user email
 * -pe openmpi numberOfProcessors  (-pe openmpi 8 - run the code in parallel on 8  processors on the Cheaha compute nodes.)
 * -l vf to the maximum memory needed for each task
 * cd to the current working directory where the job data is stored
 * Replace file.{in,out,restrt,prmtop,cmd} name with your files. 
#!/bin/bash
#$ -S /bin/bash
#
# Example Amber job submission script can be found here:
#
# Execute from the current working directory
#$ -cwd
#
# Job runtime (1 hour, at 55 minutes Amber will be notified to shut down)
#$ -l h_rt=1:00:00,s_rt=0:55:00
#$ -j y
#
# Job Name and email
#$ -N ambertest_1
#$ -M YOUR_EMAIL_ADDRESS
# Email options to determine when to send emails
#$ -m be
#
#$ -pe openmpi 4
#
# Load the appropriate module(s)
. /etc/profile.d/modules.sh
 module load amber/amber-10-intel 
#
#$ -V
#$ -l vf=1G
#
mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI  -O -i file.in -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt



Submit the script to the scheduler with

$ qsub amberSubmit

The output will be

Your job 82341234 ("ambertest_1") has been submitted


The basic usage for sander is as follows:

    sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
    [-ref refc] [-x mdcrd] [-v mdvel] [-e mden] [-inf mdinfo]

    Arguments in []'s are optional
    If an argument is not specified, the default name will be used.
    -O    overwrite all output files (the default behavior is to quit if any output files already exist)
    -i      the name of the input file (which describes the simulation options), mdin by default.
    -o     the name of the output file, mdout by default.
    -p     the parameter/topology file, prmtop by default.
    -c     the set of initial coordinates for this run, inpcrd by default.
    -r     the final set of coordinates from this MD or minimization run, restrt by default.
    -ref  reference coordinates for positional restraints, if this option is specified in the input file, refc by default.
    -x    the molecular dynamics trajectory file (if running MD), mdcrd by default.
    -v    the molecular dynamics velocities file (if running MD), mdvel by default.
    -e    a summary file of the energies (if running MD), mden by default.
    -inf  a summary file written every time energy information is printed in the output file for the current step of the minimization of MD, useful for checking on the progress of a simulation, mdinfo by default.


Some basic testing completed with data available at:http://ambermd.org/tutorials/basic/tutorial1/section3.htm

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