[gmx-developers] Re: User defined potential between specific atoms

[Berk Hess]

Hi,

Actually I forgot one line in the code, which meant -ddbc was always off.
I have fixed that now.

Berk.

Paul Whitford wrote:

> That appears to work. Thanks!
>
> -Paul
>
> Message: 4
> Date: Tue, 4 Mar 2008 10:56:16 +0100 (CET)
> From: hessb at mpip-mainz.mpg.de <mailto:hessb at mpip-mainz.mpg.de>
> Subject: Re: [gmx-developers] User defined potential between specific
>        atoms
> To: "Discussion list for GROMACS development"
>        <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
> Message-ID:
>       
>  <65059.91.32.170.145.1204624576.squirrel at squirrel.mpip-mainz.mpg.de 
> <mailto:65059.91.32.170.145.1204624576.squirrel at squirrel.mpip-mainz.mpg.de>>
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>
> >>> I am using the CVS version (downloaded yesterday).
> >>>
> >>> I am trying to include interactions between specific atoms (i.e. 
> atom 1
> >>> and
> >>> 40 are interacting and atom 30 and 80 are interacting).  I am using
> >>> "pairs"
> >>> to do this.  If I look at  large systems, where two bodies can
> >>> dissociated,
> >>> I run into a problem with dynamics load balancing.  Since "pairs" is
> >>> considered  a bonded interaction I need to set "-rdd" to a large 
> value.
> >>> If
> >>> i do this, then I can not run on many nodes because the domains are
> >>> forced
> >>> to be too large.  Is there an alternate way to include these
> >>> interactions
> >>> that won't run into this issue with DD?  I have looked at the user
> >>> defined
> >>> potentials, but it appears you can only set the form of the potential,
> >>> which
> >>> is then used in "pairs".
> >>
> >> Possibly a bond potential type 6 might work, but I can't think of a
> >> reason
> >> this wouldn't produce the same kind of problem.
> >
> > It would.
> >
> > There are two ways of solving this problem.
> > You could make these atoms separate energy groups
> > and use the energygrp_table option to supply a tabulated
> > non-bonded interaction.
> >
> > You could also simply remove the missing interactions check in the code.
> > Since somebody else also asked about this, we might consider
> > adding an option to mdrun to turn off this check, or to turn it off
> > for interactions other than normal bond, angle and dihedral potentials.
> >
> > Note that your problem is not specific for dynamic load balancing.
> > Setting -rdd much larger than your non-bonded cutoff distance
> > will kill your performance.
> >
> > Berk.
>
> I have added an option -noddbc to mdrun which turns off the check
> for pair interactions and tabulated bonds that do not generate
> exclusions.
> Please check if this options does what it should do.
> I did not have a proper test system at hand.
>
> Berk.
>
>
>
>
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