amber¶
Note
SCARF is migrating to the SLURM batch system, instructions on this page which refer to LSF commands, parameters or configuration do not apply to SLURM. Please see our SLURM page for more information.
RHEL7 Modules:
Description for amber:
Running amber: From the Amber website : “Amber” refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs
Running Amber Amber is run on the command line using an LSF job submission script Eg :
#!/bin/bash
#BSUB -n 4
#BSUB -o %J.o
#BSUB -e %J.e
#BSUB -W 60
#BSUB -x
#Load desired
imodule load amber/14
#
# Submit the job using mpirun
mpirun -lsf pmemd.MPI -i mdin -o mdout -p prmtop -c inpcrd -r restrt
Submit using:
[me@scarf]$ bsub < jcl
Where jcl is the name of the job submission script file from above. If you would like to change the number of processors to run on, please change ‘bsub -n’ parameter.
To monitor your jobs progress use the normal LSF batch commands E.g.:
[me@scarf]$ bjobs
or
[me@scarf]$ bjobs -l
Documentation for amber:
Amber team has provided a long list of tutorials which can be found on: http://ambermd.org/tutorials/