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

Berk Hess gmx3 at hotmail.com
Mon Mar 16 19:05:33 CET 2009


I think you are lucky.
The angular comm code only does not work with DD when molecules are partially over the periodic boundaries.
But I guess that in your case molecules will never cross the boundary
and therefore the comm code will work as it should.


From: x.periole at rug.nl
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] angular removal of COM and domain decomposition
Date: Mon, 16 Mar 2009 18:58:24 +0100

> 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 momentumwhile 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.


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