Purpose: molecular dynamics
Latest version: 14
Licence: Proprietary licence
Website: Reference Manual
Amber is a collection of programs for setting-up, running and analysing molecular dynamics simulations.
Amber refers both to a collection of about 50 programs for building, configuring and minimising molecular structures, setting up force fields, running simulations, analysing trajectories, and computing system properties, and to a force field for biomolecules implemented by the Amber programs.
Benchmark
Amber 14 benchmark at Collserola: actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the NPT simulation of a short peptide with ff14SB force field, TIP3P water and PME electrostatics.
LSF example script (collserola)
#!/bin/bash ## # IMPORTANT NOTICE: replace the email address # and the working directories with your own info ## # BSUB -J amber # BSUB -o amber.log # send standard output here # BSUB -e amber.err # send error output here # # Pick a queue # BSUB -q short # # Send an email notice once the job is finished # BSUB -N -u youremail@wherever # # Indicate the number of cores # BSUB -n 4 # # Pick the machine # BSUB -R collserola # Set up the environment . /opt/modules/default/init/bash module load amber/14 # Edit here to specify the filenames jobname="example" input_file="example.inp" top_file="example.top" coord_file="example.crd" output_file="example.out" # The .inp, .top and .crd files should be in the same directory # from which you submit the job (bsub < ...) # Copy input files to the /tmp volume cp $input_file $top_file $coord_file $TMPDIR cd $TMPDIR # Launch sander via MPI mpijob sander.MPI -O -i $input_file -p $top_file -c $coord_file -o $output_file # Copy the output to /cescascratch cp $output_file $SCRATCH/$jobname
Place the appropriate LSF script in a file (for instance amber.lsf) and submit the job with the command
bsub < amber.lsf