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

[James Lord]

Dear Justin & Diogo,
Thanks for your comments, I did the steps you guys mentioned to calculate
protein-suface interaction energy and expect to see "protein surface"
option upon running g_energy but it is not the case, any comments? Here is
what I did,
gedit md.mdp and then added at the end of md.mdp file
energygrps= protein surface
saved it and
grompp -f md.mdp -c  mdw.gro -t mdw.cpt -p toplgy.top -o mdnew
mdrun -s mdnew.tpr -rerun mdw.xtc

g_energy -f mdnew.edr -o energy.xvg

Thanks
James

On Sat, Oct 18, 2014 at 8:52 AM, Diogo Martins de Sá <sadiogo at mol.bio.br>
wrote:

> open your .mdp in an editor and under energygrps, add " ProteinSurface"
> after the last term.
> Run grompp using this .mdp and create a new .tpr. Then use the command
> line Justin mentioned last.
>
>
> Diogo
>
>
>
>
> ----------------------------------------------------------------------------------------------------------
>  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
>  energy
>  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
> 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.
>
>  Create a new .tpr with the .mdp file that specifies the desired
> energygrps, then:
>
>  mdrun -s new.tpr -rerun trj.xtc
>
>  -Justin
>
>  --
>  ==================================================
>
>  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
>  http://mackerell.umaryland.edu/~jalemkul
>
>  =================================================
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