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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.
+
[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.
  
 
Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.
 
Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.
  
'''Project website:'''
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'''Project website:''' http://ambermd.org/
  
 
====Load SGE module====
 
====Load SGE module====
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#$ -pe openmpi 4
 
#$ -pe openmpi 4
 
</pre>
 
</pre>
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 +
====Use Amber on the Cheaha====
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Sample Job script for Amber
 +
<pre>
 +
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
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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>
 +
#!/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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# 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 $AMBERHOME/exe/sander.MPI  -O -i file.in -o file.out -c file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref file.restrt
 +
 +
 +
</pre>
 +
 +
 +
Submit the script to the scheduler with
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<pre>
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$ qsub amberSubmit
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</pre>
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 +
The output will be
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<pre>
 +
Your job 82341234 ("ambertest_1") has been submitted
 +
</pre>
 +
 +
 +
The basic usage for sander is as follows:
 +
<pre>
 +
    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]
 +
 +
    Arguments in []'s are optional
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    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.
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    -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.
 +
 +
</pre>
 +
 +
 +
Some basic testing completed with data available at:http://ambermd.org/tutorials/basic/tutorial1/section3.htm
 +
 +
 +
[[Category:Software]][[Category:Molecular Dynamics]][[Category:Chemistry]]

Latest revision as of 11:31, 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