[gmx-users] Re: Determining energies between a solute and solvent

[Fabian Casteblanco]

Thanks.  This helps.   One more question, is it possible to further
break down the energy interactions between a piece of a protein and
another piece of the solvent?   For example, if I wanted the Cou and
vdw interactions specifically for an  -OH group on a solvent and some
chain on the solute.  I know how to do this using make_ndx for g(r)
plots but I don't see how you can apply it to energygrps on the *.mdp
file.


Thanks again for all your help.

-Fabian

On Thu, Feb 23, 2012 at 2:41 PM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> wrote:
> Thanks.   So before I run the simulation, I must use energygrps (for
> example:  energygrps: Protein SOL) in my md.mdp file so that it knows
> to write down specific interactions between the two groups.   Will
> then it simply appear when I later run g_energy?
>
> -Fabian
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------
> Short-range nonbonded interactions can be decomposed using proper energygrps in
> the .mdp file.
>
> Perhaps, but g_enemat also requires that energygrps are specified when running
> the simulation.  Otherwise, the applicable terms in the .edr file are not
> decomposed.
>
> -Justin
>
>
>
> On Thu, Feb 23, 2012 at 1:56 PM, Fabian Casteblanco
> <fabian.casteblanco at gmail.com> wrote:
>> Hello everyone,
>>
>> Is it possible to see the energy (LJ, Cou) for simply the solute
>> interacting with the solvent?
>>
>> For example, g_energy will calculate all the energies for the entire
>> system interactions which include solvent-solvent interactions.  I
>> would simply like the solute-solvent interactions or possibly simply
>> the solvent-solvent interaction energies.  I see g_enemat as a
>> possible function to use.  Is this the best way?
>>
>> Thanks.
>>
>> --
>> Best regards,
>>
>> Fabian F. Casteblanco
>> Rutgers University --
>> Chemical Engineering
>
>
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering