[gmx-users] angular removal of COM and domain decomposition

XAvier Periole x.periole at rug.nl
Mon Mar 16 18:58:24 CET 2009

> > mdrun complains when I am asking for the angular removal of the COM
> > together
> > with dynamic load balance on (with gmx-4.0.4). It says the  
> combination
> You mean domain decomposition.
Yes, sorry!

By imposed I mean that the flags are explicitly changed to do angular  
removal of
COM (remove the rotational momentum) even if it is not the case in the  
mdp file.
The code itself of not modified to do implement it!

You'd find in the lines like this:

if ( mean_field ) {
      ir->comm_mode = ecmANGULAR;
      ir->nstcomm = 1;

The question really what the code is then doing is asked to remove the  
rotational momentum
while not implemented! The code is stable for micro seconds!

It is so as the mean field stuff was imported from earlier gmx  
versions where the particule/domain
decomposition were not implemented I guess.


> > is not
> > implemented and suggests to use particle decomposition, which is
> > unfortunately
> > much much slower.
> >
> > What would happen if the use of angular removal of the COM was
> > "imposed" in a
> > subroutine implemented in an in house version (mean field boundary
> > potential)?
> > The code does not through the check_dd_restrictions so it is  
> actually
> > running but
> > it is actually difficult to see what the removal of the COM does.
> >
> > Anyone would have an idea? may be Berk?
> >
> > Thanks,
> > XAvier.
> What do you mean with "imposed"?
> If you impose it correctly, it would of course work.
> Berk
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