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Amber

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[http://ambermd.org/ "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.
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Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.
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'''Project website:''' http://ambermd.org/
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====Load SGE module====
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The following Modules files should be loaded for this package (the amber module will automatically load the openmpi module):
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For Intel:
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<pre>
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module load amber/amber-10-intel
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</pre>
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Use the '''openmpi''' parallel environment in your job script (example for a 4 slot job)
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<pre>
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#$ -pe openmpi 4
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</pre>
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====Use Amber on the Cheaha====
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Sample Job script for Amber
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<pre>
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Create a job submit script as shown below called 'amberSubmit', make sure to edit the following parameters:
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* s_rt to an appropriate soft wall time limit
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* h_rt to the maximum wall time for your job
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* -N - job name
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* -M - user email
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* -pe openmpi numberOfProcessors  (-pe openmpi 8 - run the code in parallel on 8  processors on the Cheaha compute nodes.)
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* -l vf to the maximum memory needed for each task
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* cd to the current working directory where the job data is stored
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* Replace file.{in,out,restrt,prmtop,cmd} name with your files.
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</pre>
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<pre>
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#!/bin/bash
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#$ -S /bin/bash
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#
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# Example Amber job submission script can be found here:
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#
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# Execute from the current working directory
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#$ -cwd
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#
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# Job runtime (1 hour, at 55 minutes Amber will be notified to shut down)
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#$ -l h_rt=1:00:00,s_rt=0:55:00
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#$ -j y
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#
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# Job Name and email
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#$ -N ambertest_1
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#$ -M YOUR_EMAIL_ADDRESS
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# Email options to determine when to send emails
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#$ -m be
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#
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#$ -pe openmpi 4
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#
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# Load the appropriate module(s)
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. /etc/profile.d/modules.sh
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module load amber/amber-10-intel
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#
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#$ -V
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#$ -l vf=1G
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#
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mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI  -O -i file.in -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt
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</pre>
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Submit the script to the scheduler with
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<pre>
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$ qsub amberSubmit
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</pre>
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The output will be
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<pre>
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Your job 82341234 ("ambertest_1") has been submitted
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</pre>
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The basic usage for sander is as follows:
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<pre>
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    sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
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    [-ref refc] [-x mdcrd] [-v mdvel] [-e mden] [-inf mdinfo]
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    Arguments in []'s are optional
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    If an argument is not specified, the default name will be used.
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    -O    overwrite all output files (the default behavior is to quit if any output files already exist)
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    -i      the name of the input file (which describes the simulation options), mdin by default.
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    -o    the name of the output file, mdout by default.
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    -p    the parameter/topology file, prmtop by default.
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    -c    the set of initial coordinates for this run, inpcrd by default.
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    -r    the final set of coordinates from this MD or minimization run, restrt by default.
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    -ref  reference coordinates for positional restraints, if this option is specified in the input file, refc by default.
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    -x    the molecular dynamics trajectory file (if running MD), mdcrd by default.
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    -v    the molecular dynamics velocities file (if running MD), mdvel by default.
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    -e    a summary file of the energies (if running MD), mden by default.
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    -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.
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</pre>
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Some basic testing completed with data available at:http://ambermd.org/tutorials/basic/tutorial1/section3.htm
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[[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]

Latest revision as of 12:31, 16 July 2012

This page is a Generic stub.

You can help by expanding this page..


"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/

[edit] 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

[edit] 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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