[gmx-developers] User defined potential between specific atoms

[Mark Abraham]

> 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.

Mark