# 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/

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