[gmx-developers] User defined potential between specific atoms
pwhitfor at ctbp.ucsd.edu
Tue Mar 4 00:51:36 CET 2008
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".
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