[gmx-users] Energy from a subgroup of molecules

[Justin Lemkul]

On 4/11/19 5:39 PM, paul buscemi wrote:
> Thank you for the response, Mark.
>
> I do use the rerun tactic, and this is not too bad for a small number of molecules
>
>   but is there a way to include the index information within the mdrun (rerun ) … something like
>
> gmx mdrun  -s adsorb.ener_gp.tpr  -rerun adsorb,npt.trr   - n use_only.ndx  ?
>
> or use the  indices within the grompp command ?
>

The only solution is what Mark proposed - create a .tpr file with the 
required energygrps and use mdrun -rerun. mdrun does not accept an index 
file.

-Justin

> Paul
>
>> On Apr 11, 2019, at 1:48 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>
>> You can't do that with gmx energy, as you need mdrun to understand the new
>> grouping. But making a new .tpr with the energy groups so defined permits
>> you to use gmx mdrun -rerun for such a single point energy evaluation.
>>
>> Mark
>>
>> On Wed., 10 Apr. 2019, 22:24 p buscemi, <pbuscemi at q.com> wrote:
>>
>>> Dear Users,
>>> I've performed an adsorption experiment in which a fraction of molecules
>>> in solution adsorb to a surface. I can extract the index of those adsorbed,
>>> and I can obtain the total interaction ( LJ ) of the energy group with the
>>> surface.
>>> I can estimate the average interaction of the adsorbed molecules by
>>> dividing the total energy by the number of molecules within a certain
>>> distance ( the index number )
>>> How might I use gmx energy to recalculate the interaction using the
>>> original surface but only the adsorbed molecules specified in the index
>>> file... something like
>>> "gmx energy -f starting.gro -n index.ndx"
>>>
>>> A single point calculation would be quite satisfactory.
>>> thanks
>>> Paul
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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