Assisted Model Building with Energy Refinement : “Amber” refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (AmberTools, software in the public domain) ; and a package of molecular simulation programs.

• Site web : http://ambermd.org/
• Versions installées :
  • AmberTools (libre) : v14
  • Amber (payant) : v12 avec AmberTools v13

La compilation a été faite avec le support OpenMP (utilisable pour certains programmes comme paramfit ou NAB) et MPI. Les versions MPI des programmes sont postfixés avec .MPI, par exemple sandr.MPI : il s'agit de l'installation standard d'Amber, la documentation d'Amber s'applique.

Si vous utilisez le support GPU : vous devez citer des articles dans vos publications. Voir http://ambermd.org/gpus12/ section Citing the GPU Code

Pour sélectionner la version voulue : utiliser les modules

Pour utiliser Amber 12 avec AmberTools 13 :

module load amber/12

Pour utiliser Amber 12 avec AmberTools 14 :

module load amber/12-tools14

Si vous utilisez un des programmes Amber parallélisé via OpenMP, vous devez suivre l' exemple Slurm pour OpenMP pour en tirer profit.

Une version GPU est compilée (http://ambermd.org/gpus12/). L'exécutable s'appelle pmemd.cuda et doit être exécuté sur le neoud GPU, voir les instructions s'appliquant à CALI sur la page GPU.

Vous devez charger en plus le module CUDA version 5.0 :

module load nvidia/cuda/5.0

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=02:00:00
#SBATCH --partition=normal
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2000 
topname=del
crdname=del
CURR=$(pwd)
RESTART=YES
STEP=0
FINAL=1
module load amber/16-patched-10062016
# MD are performed in Scratch 
# Export running directectory
export RUN_DIR="${HOME}/scratch/Amber/run.${SLURM_JOB_ID}.amber16.${topname}"
# Link the scratch directory to the current directory 
# Link name is related to JOB ID and NOT TO JOBNAME --> Prevent issues related to new MDs with same name
ln -sfn ${RUN_DIR} ${SLURM_JOB_ID}.results
echo ${RUN_DIR} 
# Create Scratch directory
mkdir -p ${RUN_DIR}
# Copy Topology and CRD names into Scratch directory
cp ${topname}.prmtop *.in ${RUN_DIR}
# Copy starting CRD files according to restart procedure or not
if [ $RESTART = 'YES' ]; then
    cp ${topname}_md${STEP}.rst ${RUN_DIR}/
else
    STEP=0
    cp ${topname}.inpcrd ${RUN_DIR}/
fi
# Enter into Scratch directory
cd ${RUN_DIR}
# Run calculation 
# Keep in mind: Never run a long MD into a single trajectory file - Split it into several trajectories
for i in `seq $STEP 1 $FINAL`
do
    j=$(( $i + 1 ))
    # Run MD
    pmemd -O -i md.in -o ${crdname}_md${j}.out -p $topname.prmtop -c ${crdname}_md${i}.rst -r ${crdname}_md${j}.rst -x ${crdname}_${j}.mdcrd
    # Compress mdcrd file to prevent storage issues and remove the uncompressed trajectory
    tar -zcvf ${crdname}_${j}.mdcrd.tar.gz ${crdname}_${j}.mdcrd
    rm -rf ${crdname}_${j}.mdcrd
done

#!/bin/bash
#SBATCH --nodes=1-X
#SBATCH --ntasks=X
#SBATCH --time=XX:00:00
#SBATCH --partition=normal
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=XXX 
topname=del
crdname=del
CURR=$(pwd)
RESTART=YES
STEP=0
FINAL=1
module load amber/16-patched-10062016
# MD are performed in Scratch 
# Export running directectory
export RUN_DIR="${HOME}/scratch/Amber/run.${SLURM_JOB_ID}.amber16.${topname}"
# Link the scratch directory to the current directory 
# Link name is related to JOB ID and NOT TO JOBNAME --> Prevent issues related to new MDs with same name
ln -sfn ${RUN_DIR} ${SLURM_JOB_ID}.results
echo ${RUN_DIR} 
# Create Scratch directory
mkdir -p ${RUN_DIR}
# Copy Topology and CRD names into Scratch directory
cp ${topname}.prmtop *.in ${RUN_DIR}
# Copy starting CRD files according to restart procedure or not
if [ $RESTART = 'YES' ]; then
    cp ${topname}_md${STEP}.rst ${RUN_DIR}/
else
    STEP=0
    cp ${topname}.inpcrd ${RUN_DIR}/
fi
# Enter into Scratch directory
cd ${RUN_DIR}
# Run calculation 
# Keep in mind: Never run a long MD into a single trajectory file - Split it into several trajectories
for i in `seq $STEP 1 $FINAL`
do
    j=$(( $i + 1 ))
    # Run MD
    srun premed.MPI -O -i md.in -o ${crdname}_md${j}.out -p $topname.prmtop -c ${crdname}_md${i}.rst -r ${crdname}_md${j}.rst -x ${crdname}_${j}.mdcrd
    # Compress mdcrd file to prevent storage issues and remove the uncompressed trajectory
    tar -zcvf ${crdname}_${j}.mdcrd.tar.gz ${crdname}_${j}.mdcrd
    rm -rf ${crdname}_${j}.mdcrd
done

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --time=02:00:00
#SBATCH --partition=gpu
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu
topname=del
crdname=del
CURR=$(pwd)
RESTART=YES
STEP=0
FINAL=1
module load amber/16-patched-10062016
module load nvidia/cuda/7.5
# MD are performed in Scratch 
# Export running directectory
export RUN_DIR="${HOME}/scratch/Amber/run.${SLURM_JOB_ID}.amber16.${topname}"
# Link the scratch directory to the current directory 
# Link name is related to JOB ID and NOT TO JOBNAME --> Prevent issues related to new MDs with same name
ln -sfn ${RUN_DIR} ${SLURM_JOB_ID}.results
echo ${RUN_DIR} 
# Create Scratch directory
mkdir -p ${RUN_DIR}
# Copy Topology and CRD names into Scratch directory
cp ${topname}.prmtop *.in ${RUN_DIR}
# Copy starting CRD files according to restart procedure or not
if [ $RESTART = 'YES' ]; then
    cp ${topname}_md${STEP}.rst ${RUN_DIR}/
else
    STEP=0
    cp ${topname}.inpcrd ${RUN_DIR}/
fi
# Enter into Scratch directory
cd ${RUN_DIR}
# Run calculation 
# Keep in mind: Never run a long MD into a single trajectory file - Split it into several trajectories
for i in `seq $STEP 1 $FINAL`
do
    j=$(( $i + 1 ))
    # Run MD
    pmemd.cuda -O -i md.in -o ${crdname}_md${j}.out -p $topname.prmtop -c ${crdname}_md${i}.rst -r ${crdname}_md${j}.rst -x ${crdname}_${j}.mdcrd
    # Compress mdcrd file to prevent storage issues and remove the uncompressed trajectory
    tar -zcvf ${crdname}_${j}.mdcrd.tar.gz ${crdname}_${j}.mdcrd
    rm -rf ${crdname}_${j}.mdcrd
done