[gmx-developers] User defined potential between specific atoms
mark.abraham at anu.edu.au
Tue Mar 4 01:25:21 CET 2008
> I am using the CVS version (downloaded yesterday).
> I am trying to include interactions between specific atoms (i.e. atom 1
> 40 are interacting and atom 30 and 80 are interacting). I am using
> to do this. If I look at large systems, where two bodies can
> 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.
> 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,
> 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.
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