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.
Amber vs. AmberTools
We have modules for both Amber and AmberTools available in our software stack.
- The AmberTools (module
ambertools) contain a number of tools for preparing and analysing simulations, as well assanderto perform molecular dynamics simulations, all of which are free and open source. - Amber (module
amber) contains everything that is included inambertools, but adds the advancedpmemdprogram for molecular dynamics simulations.
To see a list of installed versions and which other modules they depend on, you can use the module spider command or check the Available software page.
Loading AmberTools 21
Currently, AmberTools 21 is available on all clusters.
Non-GPU version
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 ambertools/21 source $EBROOTAMBERTOOLS/amber.sh
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, and sander.OMP
GPU version
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21 source $EBROOTAMBERTOOLS/amber.sh
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI
Loading Amber 20
Currently, Amber20 is available on all clusters.
CPU version linked with MKL
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.9-20.15
Provides all MD programs available in AmberTools/20 plus pmemd (serial) and pmemd.MPI (parallel).
GPU version
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15
Provides all MD programs available in ambertools/20 plus pmemd (serial), pmemd.MPI (parallel), pmemd.cuda (single GPU), and pmemd.cuda.MPI (multi - GPU)
Loading 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.py programs from amber/18-10-18.11 and amber/18.14-18.17 modules can not perform PB calculations. Use more recent amber/20 modules for PB calculations.
Loading Amber 16
Amber 16 is currently available on Graham only due to license restrictions. It was built with the previous system environment StdEnv/2016.4. Load StdEnv/2016.4 before loading amber/16 using the module command:
[name@server $] module load StdEnv/2016.4 [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.
#!/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 StdEnv/2016.4
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 StdEnv/2016.4
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.