<html><body><span style="font-family:Tahoma; color:#000000; font-size:10pt;"><div>open your .mdp in an editor and under energygrps, add " ProteinSurface" after the last term.</div><div>Run grompp using this .mdp and create a new .tpr. Then use the command line Justin mentioned last.</div><div><br></div><div>Diogo<br></div><div><br></div><div>----------------------------------------------------------------------------------------------------------<br> Date: Thu, 16 Oct 2014 12:07:15 -0400<br> From: Justin Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> Subject: Re: [gmx-users] How to calculate protein-surface interaction<br> energy<br> Message-ID: <<a href="mailto:543FED33.5010700@vt.edu">543FED33.5010700@vt.edu</a>><br> Content-Type: text/plain; charset=windows-1252; format=flowed<br> </div><div><br> <br> On 10/16/14 11:42 AM, James Lord wrote:<br> > Hi Justin,<br> > Sorry for not being clear, I have done the simulation without specifying<br> > the energygrps, so based on your previous comment I should use mdrun -rerun<br> > <a href="http://trj.xtc" mce_href="http://trj.xtc">trj.xtc</a> -o energy.edr -pn index.ndx? and in index file define energygrps =<br> > Protein Surface right?<br> ><br> > If not appreciate if you give an example of the command with appropriate<br> > input output etc.<br> <br> Create a new .tpr with the .mdp file that specifies the desired energygrps, then:<br> <br> mdrun -s new.tpr -rerun <a href="http://trj.xtc" mce_href="http://trj.xtc">trj.xtc</a><br> <br> -Justin<br> <br> -- <br> ==================================================<br> <br> Justin A. Lemkul, Ph.D.<br> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br> <br> Department of Pharmaceutical Sciences<br> School of Pharmacy<br> Health Sciences Facility II, Room 629<br> University of Maryland, Baltimore<br> 20 Penn St.<br> Baltimore, MD 21201<br> <br> <a href="mailto:jalemkul@outerbanks.umaryland.edu">jalemkul@outerbanks.umaryland.edu</a> | (410) 706-7441<br> <a href="http://mackerell.umaryland.edu/%7Ejalemkul" mce_href="http://mackerell.umaryland.edu/%7Ejalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br> <br> ================================================= </div></span></body></html>