Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

AMBER Example

Note: you will probably need to edit the job script for it to run succesfully.  Some things that may need to change:  your file names may be different;  your files may be stored in a different directory structure;  your job might need more time to complete; your job may require more or fewer cpus.  There may be others.

Be sure to tailor the script to suit your situation before submitting a job.  If you don't,  you may use up some of your allocation on a job that fails. If you have any questions, please contact remarks@psc.edu.

 

Files include:

amber.job, PBS script View  
md.in, input file View   
inpcrd.in, input coordinates     
prmtop, input file for molecular topology, force field, periodic box type and atom and residue names     
amber.logfile, output data View   
md.out, user readable state info and diagnostics (output) View   
mdinfo.out, latest md-format energy info (output) View   
restrt, final coordinates, velocity and box dimensions for a restart run     
amber.out, standard output and error View