Dear Andras, Concatenate all structures into one trajectory and issue gmx mdrun -rerun. That will evaluate the energies for all conformations. You will of course need a tpr file too.
Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 6 Apr 2017, at 12:39, András Ferenc WACHA <wacha.and...@ttk.mta.hu<mailto:wacha.and...@ttk.mta.hu>> wrote: Dear Gromacs Users, does someone know a way to quickly evaluate the energy of a few structures? In more detail: I have several conformations of the same peptide, stored in PDB format. In principle, they have the same topology. I want to optimize various force field parameters, which involves the need to calculate the energy multiple times, each time with different bond/angle/dihedral parameters. Currently I use a single-step mdrun (integrator = steep) and "gmx_energy" to extract the energy terms, but the overhead of calling grompp, mdrun and energy in each case for each structure is too much. In charmm you can write a script for this job: is there an equivalent in gromacs without the overheads? Thank you in advance. Best regards, András Wacha -- András Ferenc Wacha, PhD research fellow, CREDO instrument responsible Biological Nanochemistry Research Group Institute of Materials and Environmental Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences (RCNS HAS) Magyar tudósok körútja 2. H-1117 Budapest, Hungary Phone: +36-1-382-6427 Web: http://bionano.ttk.mta.hu, CREDO SAXS instrument: http://credo.ttk.mta.hu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.