Thanks very much for all your suggestions! > One way that you might approach it is to use mdrun -rerun. You could order > the > lipids with respect to the lipid of interest, such that the reference lipid > is > always molecule N and the nearest lipid is always written as N+1 in the > ordered > trajectory file. Then use normal index groups as your energygrps in the .mdp > file and recalculate the energies with mdrun -rerun.
Do I understand correctly that in the ordered trajectory each frame should have lipids ordered is such a way that in any two frames N and M the lipids with n and n + 1 indices should be neighbors but these need not necessarily be the same lipids in two frames ? Could you also please inform what command may one use to reorder lipids in a trajectory per frame? Thanks very much for all the help. > Date: Mon, 22 Jul 2013 08:04:27 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/22/13 6:20 AM, Davit Hakobyan wrote: > > Dear Gromacs Users, > > > > Is there a way in Gromacs to calculate the interaction energy between any > > two neighbor lipids dynamically? Since the neighbor lipids change over time > > in the trajectory file specifying a static energy groups in the input > > script will not help. > > > > Is there a way to accomplish this? > > > > One could use the g_select tool to define dynamic groups but again the > > energy file needs a predefined groups which probably makes the g_select > > tool useless in this case? > > > > One way that you might approach it is to use mdrun -rerun. You could order > the > lipids with respect to the lipid of interest, such that the reference lipid > is > always molecule N and the nearest lipid is always written as N+1 in the > ordered > trajectory file. Then use normal index groups as your energygrps in the .mdp > file and recalculate the energies with mdrun -rerun. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
