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

[Paul Whitford]

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
Subject: Re: [gmx-developers] User defined potential between specific
       atoms
To: "Discussion list for GROMACS development"
       <gmx-developers at gromacs.org>
Message-ID:
       <65059.91.32.170.145.1204624576.squirrel at squirrel.mpip-mainz.mpg.de>
Content-Type: text/plain;charset=iso-8859-1

>>> 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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