[gmx-users] Fast energy evaluation

[Mark Abraham]

Hi,

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

On Thu, Apr 6, 2017 at 1:00 PM Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> 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 <018-471%2045%2039>
> 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 <+36%201%20382%206427>
> Web: http://bionano.ttk.mta.hu,
> CREDO SAXS instrument: http://credo.ttk.mta.hu
>
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