Hi Diogo, Yes that is what I have at the end of top file. ps: Sorry Justin I just saw your previous email. Cheers James
On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá <sadi...@mol.bio.br> wrote: > At the end of your topology file, what molecules do you have written > down? > You should have something like: > Protein > Surface > SOL > Ion (if you needed to equilibrate system) > > > Diogo > > > > > ---------------------------------------------------------------------------------------------------------- > Date: Thu, 16 Oct 2014 12:07:15 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] How to calculate protein-surface interaction > energy > Message-ID: <543fed33.5010...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================= > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.