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Amber

Installed versions

Resource Version
Dardel/cpe23.12 22, 24

General information

"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. For more information see: http://ambermd.org

How to use

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.

The term Amber is also used to refer to the empirical force fields that are implemented in Amber. It should be recognized however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs.

In order to use Amber22, you need to 

$ ml amber/22-cpeGNU-23.12-ambertools-22

To check for other available versions of Amber, you can use

$ module avail amber

Note

Note that you need to load the PDC module before loading the amber module

This will append the directory containing all Amber executables to your PATH variable, and set various library paths. Many of the Amber subprograms come in serial, parallel and other versions, including: * sander, sander.MPI, sander.LES, sander.LES.MPI * pmemd, pmemd.MPI * cpptraj, cpptraj.MPI * MMPBSA.py, MMPBSA.py.MPI Here is an example batch script for a parallel execution of pmemd.MPI: :language: text For running subprograms that rely on the Python interface to Amber, for example MMPBSA, one needs to load the appropriate Anaconda Python distributions and activate the mpi4py conda environment.

Here is an example batch script for a parallel execution of MMPBSA.py.MPI:

#!/bin/bash -l

# Name of you allocation
#SBATCH -A XXXX-XX-XX
# Name of the job
#SBATCH -J myjob
# Partition
#SBATCH -p main
# Maximum wallclock time of job
#SBATCH -t 02:00:00
# Total number of nodes
#SBATCH --nodes=2
# Number of MPI processes per node
#SBATCH --ntasks-per-node=16
module load amber/22-cpeGNU-23.12-ambertools-22
# we run on two nodes with 16 cores per node
srun pmemd.MPI -O -i input.in -o output.out -p prm.prmtop -c coords.rst -r restart.rst -x traj.mdcrd


#!/bin/bash -l

# Name of you allocation
#SBATCH -A XXXX-XX-XX
# Name of the job
#SBATCH -J myjob
# Maximum wallclock time of job
#SBATCH -t 02:00:00
# Partition
#SBATCH -p main
# Total number of nodes
#SBATCH --nodes=2
# Number of MPI processes per node
#SBATCH --ntasks-per-node=32
module load amber/22-cpeGNU-23.12-ambertools-22
# MMGBSA calculation of a previously generated trajectory
srun MMPBSA.py.MPI -O -i MMPBSA.in -o MMPBSA.dat -sp solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y trajectory.nc >& MMPBSA.log