AMBER
Introduction[edit]
Amber is the collective name for a suite of programs that allow users to perform molecular dynamics simulations, particularly on biomolecules. None of the individual programs carry this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.
Running Amber 18[edit]
Currently, versions 18 and 18.10-18.11 are available on all clusters.
Non-GPU versions
module load gcc/5.4.0 openmpi/2.1.1 amber/18 scipy-stack/2019a
or
module load gcc/5.4.0 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a
GPU versions:
module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18 scipy-stack/2019a
or
module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a
Running Amber 16[edit]
Amber 16 is currently installed only on Graham due to license restrictions. Load it using the module command:
[name@server $] module load amber/16
This version does not support some Python functionality of Amber.
Job submission[edit]
For a general discussion about submitting jobs, see Running jobs.
The following example is a sander serial job script. The input files are in.md, crd.md.23, prmtop.
#!/bin/bash
#SBATCH --ntasks=1 # 1 cpu, serial job
#SBATCH --mem-per-cpu=2G # memory per cpu
#SBATCH --time=00-01:00 # time (DD-HH:MM)
#SBATCH --output=cytosine.log # .log file from scheduler
module load amber/16
sander -O -i in.md -c crd.md.23 -o cytosine.out
The following example is a sander.MPI parallel job script:
#!/bin/bash
#SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, MPI job
#SBATCH --mem-per-cpu=2G # memory, should be less than 4G
#SBATCH --time=00-01:00 # time (DD-HH:MM)
#SBATCH --output=sodium.log # output .log file
module load amber/16
srun sander.MPI -ng 2 -groupfile groups
You can modify the script to fit your job's requirements for compute resources. See Running jobs.
Examples[edit]
Sample *.sh and input files can be found on Graham under
/home/jemmyhu/tests/test_Amber/