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

Diogo Martins de Sá sadiogo at mol.bio.br
Sun Oct 19 03:15:17 CEST 2014

At the end of your topology file, what molecules do you have written
You should have something like:
Ion (if you needed to equilibrate system)


 Date: Thu, 16 Oct 2014 12:07:15 -0400
 From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org
 Subject: Re: [gmx-users] How to calculate protein-surface interaction
 Message-ID: <543FED33.5010700 at vt.edu>
 Content-Type: text/plain; charset=windows-1252; format=flowed

 On 10/16/14 11:42 AM, James Lord wrote:
 > Hi Justin,
 > Sorry for not being clear, I have done the simulation without
 > the energygrps, so based on your previous comment I should use mdrun
 > 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
 > input output etc.
 Create a new .tpr with the .mdp file that specifies the desired
energygrps, then:
 mdrun -s new.tpr -rerun trj.xtc
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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