Hallo Maybe try comm-grps = protein all-but-protein (all-but-protein being all atoms except those contained in protein)
I guess this problem is brought about by the way VCM groups are constructed: src/kernel/readir.c, do_numbering(), line 1081 in 4.0.3 if (grps->nr == 1) { groups->ngrpnr[gtype] = 0; groups->grpnr[gtype] = NULL; } else { groups->ngrpnr[gtype] = natoms; snew(groups->grpnr[gtype],natoms); for(j=0; (j<natoms); j++) { groups->grpnr[gtype][j] = cbuf[j]; } } Indeed, grps->nr==1. If you add another VCM group, then grps->nr==2 and the else branch is executed, which should do the trick, I believe. At the same time, the removal of rotation of a group including almost all atoms (solvent) should have a negligible effect on the velocities. I'm testing that right now, because I've had the same problem, trying to keep a DNA oligomer in the center of the box. (I'm aware of the possible appearance of artifacts...) If this doesn't work, then I'm going to try to hack do_numbering() a bit. tomas XAvier Periole wrote: > > Dears, > > I am asking for the angular removal of the COM motion of a protein > assembly > in gromacs-4.0.4. > > - grompp gives a strange warning: > > checking input for internal consistency... > > WARNING 3 [file md.mdp, line unknown]: > Removing the rotation around the center of mass in a periodic system > (this is not a problem when you have only one molecule). > > - the lines are: > > nstcomm = 1 > comm-mode = angular > comm-grps = protein > > > Then the nstcomm and comm-mode appear to be correctly defined in the > tpr file > generated. However during the run the angular removal of the COM is > clearly not > done. The protein assembly is rotating ... > > Any reason for this? > > XAvier. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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/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/mailing_lists/users.php