Thanks so much for the suggestion. By using the command:
trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o system_ordered.trr the resulting system_ordered.trr indeed contained lipids 2,3,4... in the closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm). Then by specifying new energy groups like lipid1, lipid2, etc the energy file was generated with the "rerun" flag: mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr many warnings were shown like: WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=31000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=32000. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file system_ordered.edr Found: step=-1, nre=68, nblock=0, time=33000. Trying to skip frame expect a crash though Do these warnings point to some error? >From the generated energy file one optionally could select not only coulomb >and vdw terms between the goups lipid1, lipid2 and lipid3 but also between >lipid1 and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ >-30-40 kJ/mol. Since the latter is the vdw energy of a lipid with itself >should one understand this value as the interaction between different atoms of >one lipid? The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from the feeling that these vdw numbers are ~ twice larger than they should does this procedure contain some obvious problems? Thanks very much for all the help. > Date: Mon, 22 Jul 2013 08:39:27 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/22/13 8:37 AM, Davit Hakobyan wrote: > > 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 ? > > > > Yes. > > > Could you also please inform what command may one use to reorder lipids in > > a trajectory per frame? > > > > Start by reading trjorder -h. The exact approach depends on what you're > dealing > with. > > -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
