[gmx-users] How to calculate protein-surface interaction energy
jjamesgreen110 at gmail.com
Thu Oct 16 17:42:03 CEST 2014
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.
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
>> a bit more what to do? if I want to have total energy= vdw and
> energygrps = Protein Surface
> or whatever the names should be.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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