[gmx-users] How to calculate protein-surface interaction energy

[James Lord]

Hi Justin,
Sorry for not being clear, I have done the simulation without specifying
the energygrps, so based on your previous comment I should use mdrun -rerun
trj.xtc -o energy.edr -pn index.ndx?  and in index file define energygrps =
Protein Surface right?

If not appreciate if you give an example of the command with appropriate
input output etc.
Cheers
James

On Fri, Oct 17, 2014 at 3:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/16/14 10:47 AM, James Lord wrote:
>
>> Hi Justin,
>> Thanks, the .mdp is the same as your tutorial for lysozyme, Can you
>> explain
>> a bit more what to do? if I want to have total energy= vdw and
>> electrostatic?
>>
>
> energygrps = Protein Surface
>
> or whatever the names should be.
>
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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