[gmx-users] problem with center of mass removal, rest-group, all gmx versions

[Daniel Larsson]

On Dec 10, 2008, at 7:45 , Michael Brunsteiner wrote:

> In ALL my md.log files is see the following output:
>
> We have the following groups for center of mass motion removal:
>  0:  rest, initial mass: 163113
> There are: 6508 Atoms
>
> in the mdp-documentation it says:
>
> comm_grps:
>    group(s) for center of mass motion removal, default is the whole  
> system
>
> I only now noticed that i never set comm_grps explicitly,
> assuming that the default (System) is ok, the comm_mode i typically
> set to Linear and nst_comm to either 100 or 1, or I leave these
> commands out altogether assuming that the defaults are ok ...
> system blows up in each case.
> My system has much more than 6508 atoms, and none of the groups in the
> ndx file contains 6508 atoms, and i double and triple checked that
> there is not a sigle atom that is NOT member of some group in the
> ndx file ... so what is this "rest" group??  it is apparently
> made automatically by grompp or mdrun. I can imagine that constraining
> the center of mass of a (possibly randomly chosen) subgroup of
> atoms can cause instabilities, has anybody observed something
> like this before ??

If you suspect that the choice of atom group for center of mass motion  
removal is the problem, why don't you go ahead and set the group  
explicitly by giving an index file to grompp and specify the group in  
the mdp file.

And as always when it comes to problems of systems blowing up, double  
and triple check the starting structure for clashes.

More information on the wiki, e.g. this page: http://wiki.gromacs.org/index.php/Errors