[gmx-users] Energy from a subgroup of molecules

[paul buscemi]

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 ?


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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