[gmx-users] Fast energy evaluation

[Peter Kroon]

Hi,

In addition to Erik's tip: once you have a tpr (made once with grompp),
change it for every iteration by writing your new parameters directly to
the tpr file, bypassing grompp entirely. This will require a custom
script and might not be completely trivial though.

Peter


On 06-04-17 13:15, Mark Abraham wrote:
> 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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