AMBER

Introduction

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

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

Known issues

MMPBSA program in AMBER/18-10-18.11 module has an issue with PB calculations. Use AMBER/18 or AMBER/16 modules for MMPBSA calculations.

Running Amber 16

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

For a general discussion about submitting jobs, see Running jobs.

In examples below, change the module load command to the one shown above if you wish to use the newer version.

The following example is a sander serial job script. The input files are in.md, crd.md.23, prmtop.

File : amber_serial.sh

#!/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:

File : amber_parallel.sh

#!/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

Sample *.sh and input files can be found on Graham under

/home/jemmyhu/tests/test_Amber/

Message Passing Interface