Amber

"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)
 * 1) $ -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.

. /etc/profile.d/modules.sh module load amber/amber-10-intel 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
 * 1) !/bin/bash
 * 2) $ -S /bin/bash
 * 3) Example Amber job submission script can be found here:
 * 4) Execute from the current working directory
 * 5) $ -cwd
 * 6) Job runtime (1 hour, at 55 minutes Amber will be notified to shut down)
 * 7) $ -l h_rt=1:00:00,s_rt=0:55:00
 * 8) $ -j y
 * 9) Job Name and email
 * 10) $ -N ambertest_1
 * 11) $ -M YOUR_EMAIL_ADDRESS
 * 12) Email options to determine when to send emails
 * 13) $ -m be
 * 14) $ -pe openmpi 4
 * 15) Load the appropriate module(s)
 * 1) Email options to determine when to send emails
 * 2) $ -m be
 * 3) $ -pe openmpi 4
 * 4) Load the appropriate module(s)
 * 1) Load the appropriate module(s)
 * 1) Load the appropriate module(s)
 * 1) $ -V
 * 2) $ -l vf=1G
 * 1) $ -l vf=1G

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