Hi,
I am trying to look at the free energy differences as a function of
end-to-end distance of peptides in water. I am running a set of simulations
with the two atoms of interest joined by a type 2 constraint, with the length
varying from 0.5 to 3 nm. However, these simulations all explode, even though
I am starting with conformations from an unconstrained simulation that are
taken through another round of energy minimization and relaxtion before running
the constrained simulations.
There is an mdrun option, -rcon, that I have not been setting. I read
this as the distance over which atoms interacting through the constraint will
be communicated between processors for the P-LINC algorithm. since some of the
end-to-end distances can be relatively large, I was wondering if, in principle,
I should be setting -rcon to the constarint distance +1 nm to ensure that the
constraint is not randomly disappearing from consideration when the two ends of
the peptide are in different domains.
Thanks for any insights.
Warren Gallin--
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