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

[XAvier Periole]

Indeed we are lucky then!
In the mean field there no periodic boundary, the system is spherical.

Thanks.
XAvier.

On Mar 16, 2009, at 7:05 PM, Berk Hess wrote:

> Hi,
>
> 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.
>
> Berk
>
> 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 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.
>
> XAvier.
>
> > 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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