Amber

Description

According to the Amber manual, Amber is a package of programs for molecular dynamics of biomolecules. Amber20 includes the pmemd program, which offers superior performance on multiple CPUs and significant acceleration on GPUs.

Available Versions

  • amber/20

  • amber/24

Additional Modules

When loading version 20 of the Amber module, the following modules are loaded automatically:

  • cmake/3.9.0

  • openmpi/4.0.1 (for MPI support)

When loading version 24 of the Amber module, the following modules are loaded automatically:

  • cmake/4.0.3

  • intel/oneapi/hpc/2025.2 (for MPI support)

  • cuda/12.4 (for versions with GPU support)

Serial Job Submission

submit_amber_serial.sh
#!/bin/bash
#SBATCH -J amber_serial
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 24:00:00
#SBATCH --mem=8G

export INPUT="tleap.in"
export OUTPUT="*"

module load amber/20
job-nanny tleap -f tleap.in

MPI Job Submission

submit_amber_mpi.sh
#!/bin/bash
#SBATCH -J amber_mpi
#SBATCH -N 2
#SBATCH --ntasks-per-node=28
#SBATCH -t 48:00:00
#SBATCH --mem-per-cpu=2G

export INPUT="input.prmtop input.inpcrd"
export OUTPUT="output.mdcrd output.mdinfo"

module load amber/24
job-nanny mpirun -n 56 pmemd.MPI -O -i input.in -o output.out \
         -p input.prmtop -c input.inpcrd -r restart.rst \
         -x output.mdcrd

GPU Job Submission

submit_amber_gpu.sh
#!/bin/bash
#SBATCH -J amber_gpu
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 24:00:00
#SBATCH --mem=32G

export INPUT="input.prmtop input.inpcrd"
export OUTPUT="output.mdcrd output.mdinfo"

module load amber/24
job-nanny pmemd.cuda -O -i input.in -o output.out \
         -p input.prmtop -c input.inpcrd -r restart.rst \
         -x output.mdcrd

MPI + GPU Job Submission

submit_amber_mpi_gpu.sh
#!/bin/bash
#SBATCH -J amber_mpi_gpu
#SBATCH -p gpu
#SBATCH --gres=gpu:4
#SBATCH -N 2
#SBATCH --ntasks-per-node=4
#SBATCH -t 72:00:00
#SBATCH --mem=64G

export INPUT="input.prmtop input.inpcrd"
export OUTPUT="output.mdcrd output.mdinfo"

module load amber/24
job-nanny mpirun -n 8 pmemd.cuda.MPI -O -i input.in -o output.out \
         -p input.prmtop -c input.inpcrd -r restart.rst \
         -x output.mdcrd

Example Input File

tleap.in
source leaprc.protein.ff14SB
source leaprc.water.tip3p
protein = loadPdb "protein.pdb"
solvateBox protein TIP3PBOX 10.0
addIons protein Cl- 0
saveAmberParm protein protein.prmtop protein.inpcrd
quit

References

See also