Amber
Amber 14, 16 and 18 is available to all users of computing machines in PSNC.
Amber is about two things: a set of molecular mechanical force fields for biomolecular simulations (which are in the public domain and used in various simulation programs) and a package of molecular simulation programs that includes source codes and demos.
To run the sample test of the Amber software you need to:
load module:
module load amber
Sample SLURM startup script:
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=4gb
#SBATCH --time=01:00:00
# Set paths or load appropriate modules
module load amber/14
# Set the $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID
# We set application variables
export SCR=${TMPDIR}
# We set auxiliary variables
INPUT_DIR="input"
OUTPUT_DIR="output"
OUTPUT_FILE="OUTPUT"
# Create a temporary directory
mkdir -p ${TMPDIR}
# Copy the input data to the directory pointed to by the $TMPDIR variable
cp ${SLURM_SUBMIT_DIR}/${INPUT_DIR}/* ${TMPDIR}
# Go to the $TMPDIR directory
cd $TMPDIR
# We do the calculations
sander.MPI -O -i 01_Min.in -o 01_Min.out -p prmtop -c inpcrd -r 01_Min.rst -inf 01_Min.mdinfo
sander.MPI -O -i 02_Heat.in -o 02_Heat.out -p prmtop -c 01_Min.rst -r 02_Heat.rst -x 02_Heat.mdcrd -inf 02_Heat.mdinfo
sander.MPI -O -i 03_Prod.in -o 03_Prod.out -p prmtop -c 02_Heat.rst -r 03_Prod.rst -x 03_Prod.mdcrd -inf 03_Prod.info
# Footer
cat << EOF
-------------------------------------------------- ---------------
End of calculations [$(date)].
-------------------------------------------------- ---------------
EOF
# We finish the calculations, copy the contents of the $TMPDIR/output directory
# to the directory from which the job was queued.
mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR}
cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/
# Clear working directory
rm -rf $TMPDIR
The script is divided into 3 parts:
1. Run minimization 2. Run heating MD 3. Run production MD
Below is a package with files that should be in the input directory.