[gmx-users] Fast energy evaluation

Erik Marklund erik.marklund at kemi.uu.se
Thu Apr 6 13:00:39 CEST 2017

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 Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 6 Apr 2017, at 12:39, András Ferenc WACHA <wacha.andras at ttk.mta.hu<mailto:wacha.andras at 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-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.

More information about the gromacs.org_gmx-users mailing list