AFAIK, the residue names in the mdrun output .gro file are those of the structure file you gave to grompp.
Mark On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn <rvanl...@gmail.com> wrote: > Hello, > > I am simulating a lipid bilayer and wish to apply position restraints to > only a subset of the lipids in the bilayer. Since position restraints are > applied to all molecules of the same molecule type, I defined a new > molecule type (DOPR) which is identical to my lipid species (DOPC) by > copying the lipid itp file, renaming it and renaming the corresponding > molecule type. I then manually edited a starting .gro file to change a > subset of the DOPC molecules to DOPR, edited my topology, > renumbered/reordered, etc. I also recreated the index file to account for > the new molecules so that temperature coupling could be used correctly. > > Everything seemed ok when I ran the mdrun - grompp didn't complain, the > program ran normally, the output trajectory clearly used the correct > position restraints, etc. The weird part, though, is that the output .gro > file at the end of the simulation only had DOPC molecules in it - the DOPR > molecules that I had renamed by hand had somehow been output as DOPC > instead. Positions, number of atoms, everything else was fine, just the > name of the residues was different. I can't figure out why this is > happening. It was reproducible across both GMX 4.5.5 / 4.6 and multiple > different starting files. > > It's not a huge issue since the trajectories themselves are fine, I'm just > worried this issue might indicate other, less obvious problems. A snippet > of the topol file is below if that is helpful. > > Any suggestions / advice would be appreciated! > > ******************************** > #include "forcefield.itp > #include "dopc.itp" > > #ifdef POSRES > #include "dopc-posre.itp" > #endif > > ; Always include DOPR restraints for restrained lipids > #include "dopc_restrained.itp" > #include "dopr-posre.itp" > > #include "spc.itp" > #include "ions.itp" > > [ system ] > ; Name > frame t= 1.000 in water > > [ molecules ] > ; Compound #mols > DOPC 398 > DOPR 2 > SOL 63882 > NA 179 > CL 179 > ********************************* > > Thanks, > Reid > -- > 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