> Hi, > > I would like to thank you and David for the answers. By "multiple > programs", > I meant batch scripts that contain other preprocessing/postprocessing > programs besides mdrun (like grompp, pdb2gmx,...) - so this would be a > case > in which the processing is done in multiple steps. I asked this because > we're especially interested in multi-step processes (workflows); and in > the > Gromacs tutorials most of the examples are like this (some other programs > are invoked before and after mdrun).
Well a typical replica-exchange MD workflow for me includes a script that takes some PDB file with the right protein configuration, and runs pdb2gmx, editconf, genion and grompp using expect and various command line flags to generate files suitable for starting equilibrations. These tend to get run in multiple batch scripts, then another script to make the simulation run input files. Then a batch script that runs a simulation, optionally using tpbconv to create continuation run input files as required, and resubmits a copy of itself afterwards at the end, to create an infinite loop until user interaction or machine crash intervenes. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
