[gmx-users] angular COM removal

Tomas Kubar tomas at molecular.cz
Tue Aug 11 19:07:20 CEST 2009


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;
    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.


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.
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