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Amber

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General Description

Assisted Model Building with Energy Refinement (AMBER) is a software suite used for the simulation of biomolecules.

Basic Usage

Pre- and post-processing tools of Amber are available after loading its module:

module load amber

A job script example for running parallel version of Amber:

#!/bin/csh
# Example for 24 processors.
#$ -N amber_job_name
#$ -pe smp 24
#$ -M netid@nd.edu
#$ -m abe
# Do not set automatic restart as Amber does not recover well

module load amber/16.0

mpirun -np $NSLOTS $AMBERHOME/exe/sander.MPI  -O -i file.in -o file.out -c file.restrt -p file.prmtop  -r file.restrt -x file.cmd -ref file.restrt

Replace file.{in,out,restrt,prmtop,cmd} name with your files.

A job script example for running MMPBSA:

#!/bin/csh
#$ -M netid@nd.edu    # Email address for job notification
#$ -m abe             # Send mail when job begins, ends and aborts
#$ -N mmpbsa          # Specify job name
#$ -q long
#$ -pe smp 1

module load amber/16.0
MMPBSA -O -i test.in -o FINAL_RESULTS_DEC23.dat -do FINAL_DECOMP_DEC23.dat -sp npc12ncw.top -cp npc12ncnw.top -rp npc1ncnw.top -lp npc2ncnw.top -y npc12ncwmd2.crd.gz npc12ncwmd3.crd.gz

For further information, please consult the Amber documentation: http://ambermd.org/

Amber with GPU Acceleration

More information on Amber acceleration using GPU can be found here. To run the GPU version of Amber, please send a request to CRCSupport@nd.edu. The following is a job script example for running Amber 14.0 accelerated with GPU:

#!/bin/csh
#$ -M netid@nd.edu    # Email address for job notification
#$ -m bea             # Send mail when job begins, ends and aborts
#$ -N Amber-GPU       # Specify job name
#$ -q gpu             # Run on the GPU cluster
#$ -pe smp 4

module load amber/16.0  # Load Amber accelerated with GPU

cat > mdin <<EOF
 short md, nve ensemble
 &cntrl
   ntx=7, irest=1,
   ntc=2, ntf=2, tol=0.0000001,
   nstlim=20, ntt=0,
   ntpr=1, ntwr=10000,
   dt=0.001,
 /
 &ewald
  NFFT1=72,NFFT2=64,NFFT3=60,
 /
EOF


pmemd.cuda -O -o md.out -c md12.x -r restrt -x mdcrd # 

Further Information

  • Amber16 User's Manual [1]
  • Amber Tools Version User's Manual [2]
  • See the official website: [3]