[gmx-users] Energy between desired selected molecules

[Justin Lemkul]

On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
> Thank you Mark, I see. But what is the solution then? The way you proposed
>
> ''You can make a new .tpr file with those
> energy groups and use mdrun -rerun on the old trajectory, however.''
>
>  is not my answer, since I do not want the energy for a ''group'' of
> molecules, rather for specified combination of few molecules I define from
> g_select.
>

The only function available is to define energygrps in the .mdp file, supply an 
index file with those groups (e.g. from g_select) and do as Mark says and 
re-calculate those interaction energies with mdrun -rerun on the existing 
trajectory.  The short-range nonbonded interaction energies between those groups 
will be written to their own terms in a new .edr file.

-Justin

>
> Best regards
>
>
> On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> The .edr file contains only what was written during the simulation, and
>> that was for any energy groups defined before that run. You're trying to
>> ask it to make an arbitrary repartition, which it can't do unless it
>> recorded every component of the energy for every frame (which would take
>> forever and use lots of disk). You can make a new .tpr file with those
>> energy groups and use mdrun -rerun on the old trajectory, however.
>>
>> Mark
>>
>> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
>> wrote:
>>
>>> Hi
>>>
>>> Does someone know how to obtain energy between specific molecules in the
>>> system?
>>>
>>> What I did and seems not be correct is:
>>> 1- I obtained the molecules I wanted to look at:
>>> g_select_mpi -f 600gro.gro -s production.tpr -on
>>>
>>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
>>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
>>>
>>> 3- Finally put the created .tpr file as an input for g_energy
>>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
>>>
>>> But that is not the solution, since it gives energy for whole system.
>>> Best regards
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================