AMBER-Teaching
Category
Chemistry
Program On
Teaching
Version
14
Author / Distributor
Please see http://ambermd.org/#developers
When citing Amber14 or AmberTools15 please use the following: D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco.
Description
From 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."
Running Program
Also refer to Running Jobs on the teaching cluster.
AMBER14 and AmberTools 15
AMBER14 and AmberTools 15 were compiled with the GNU 5.4.0 compiler suite (fully patched as of 1/20/2019). The MPI version uses MPICH 3.2 and the CUDA version uses the toolkit version 7.5.18.
To use this version of AMBER, first load the Amber/14-at15 module with
ml Amber/14-at15
This module will automatically load its dependencies, namely GCC/5.4.0-2.26, MPICH/3.2-GCC-5.4.0-2.26, and CUDA/7.5.18.
1. Running the MPI version:
In the example below the name of the input file is prod.in.
Example of shell script (submpi.sh) to run Amber14 in the batch queue, using 96 processes:
#!/bin/bash
#SBATCH --job-name=amberjob
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=4
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Amberjob.%j.out
#SBATCH --error=Amberjob.%j.err
cd $SLURM_SUBMIT_DIR
ml Amber/14-at15
source ${AMBERHOME}/amber.sh
mpiexec $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd
Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed.
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Sample job submission command:
sbatch submpi.sh
2. Running the CUDA version:
In the example below the name of the input file is prod.in.
Example of shell script (subcuda.sh) to run AMBER14 in the GPU queue (gpu), using one GPU card:
#!/bin/bash
#SBATCH --job-name=amberjob
#SBATCH --partition=gpu
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=2
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Amberjob.%j.out
#SBATCH --error=Amberjob.%j.err
cd $SLURM_SUBMIT_DIR
ml Amber/14-at15
source ${AMBERHOME}/amber.sh
$AMBERHOME/bin/pmemd.cuda -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd
Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed.
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Sample job submission command:
sbatch subcuda.sh
Documentation
Please see http://ambermd.org/
Installation
Source code compiled with GNU 5.4.0 compilers. The MPI version uses MPICH2 3.2 and the CUDA version uses the toolkit version 7.5.18.
System
64-bit Linux