Amber

Amber - Assisted Model Building with Energy Refinement - is a suite of biomolecular simulation programs.

External Links:
Amber website
Amber Tutorials

Two Amber modules are available on Hazel:

Here we provide some sample files (from AMBER) and give instructions how to run the most popular AMBER executables on the Hazel cluster using the recommended amber-slurm/26 module. However, many more exeutable are available for use, and can be seen with:

ls /usr/local/apps/ambertools26/bin

ls /usr/local/apps/pmemd26/bin

If you need the older amber/25 module instead (remember: launch its MPI executables with mpirun, not srun), its executables can be seen with:

ls /usr/local/apps/ambertools25/bin

ls /usr/local/apps/pmemd24/bin

Typically, it's not a good idea to run Amber from your /home directory, as its output can easily overflow your quota. Instead make a directory in your group's /share directory and run Amber from there. However, be aware that files in /share are NOT backed up and files which have not been accessed in some time are automatically deleted.

Not all the Amber executables are parallel or run on GPUs. Some have serial, parallel, and GPU versions. For example, sander.MPI is a parallel executable, and sander is serial. pmemd.cuda.MPI is parallelized and runs on GPUs.

The A100 and H100 nodes should be reserved for jobs that run quantum-mechanics applications, or need double-precision MD.

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Here's an example job submission file

#!/bin/bash
#SBATCH --ntasks=8
#SBATCH --output=out.%j
#SBATCH --error=err.%j
#SBATCH --time=00:05:00
source ~/.bashrc
cd /share/$GROUP/$USER
module load amber-slurm/26
cp /usr/local/apps/ambertools25/test/sander_OIN_MPI/trpcge.crds .
cp /usr/local/apps/ambertools25/test/sander_OIN_MPI/TC5b.top .
cp /usr/local/apps/amber20/test/sander_OIN_MPI/gbin .
srun sander.MPI -O -i gbin -c trpcge.crds -p TC5b.top -o sander.out

If the above script is in a file named "test.sh", you would submit it by

sbatch test.sh

sander and pmemd (pmemd.cuda & pmemd.cuda.MPI) can run on GPU nodes. The A100 and H100 nodes should be reserved for running quantum mechanical jobs, or for running double-precision MD.

Please use the following mdin to run the following example:

short md, nve ensemble
&cntrl
ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=10, ntt=0,
ntpr=1, ntwr=10000,
dt=0.001, ig=71277,
efx=1,efy=1,efz=1,efphase=2,effreq=2,
/
&ewald
nfft1=60, nfft2=60, nfft3=60,netfrc=0,
/

Use the following submission script for the test.

#!/bin/bash
#SBATCH --ntasks=2
#SBATCH --time=00:05:00
#SBATCH --gres=gpu:a10:2
#SBATCH --partition=gpu_partners
#SBATCH --qos=short_gpu
#SBATCH --output=out.%j
#SBATCH --error=err.%j
source ~/.bashrc
cd /share/$GROUP/$USER
module load amber-slurm/26
cp /usr/local/apps/pmemd24/test/cuda/4096wat/prmtop .
cp /usr/local/apps/pmemd24/test/cuda/4096wat/eq1.x .
srun pmemd.cuda.MPI -O -i mdin -c eq1.x -p prmtop -o mdout

If the above script is in a file named "test.sh", you would submit it by

sbatch test.sh

For users holding an AMBER license who want to build their own AMBER26 executables from source: download AmberTools26 and pmemd26 separately from ambermd.org (they require separate license forms). Load the following before building:

module load cmake/3.18.2
module load openmpi-gcc/openmpi5.0.9-gcc11.5.0-slurm
module load cuda/12.6

Use the run_cmake script bundled in each source tree's build/ directory rather than invoking cmake directly — edit it to set AMBER_PREFIX to your install location and enable -DMPI=TRUE (and -DCUDA=TRUE for pmemd). Before running make, check cmake.log for MPI: ON to confirm it linked against the Slurm-aware OpenMPI rather than a different MPI build.

Note: if building a GPU-enabled binary, do not add the CUDA toolkit's stubs/ directory to LD_LIBRARY_PATH in any runtime environment or modulefile — it will shadow the real GPU driver and cause pmemd.cuda to fail with "CUDA driver is a stub library". The stub is only needed for compiling without a physical GPU present, never for running an already-built GPU binary.

Last modified: September 01 2026 21:22:40.