yes it will, and so will it affect the profile if water molecules or
ions go in when both chains are absent.
You'll need to determine what question you are trying to answer and
also think pretty hard about what your PMF really means in the context
of this system.
Chris.
-- original message --
Hi Chris
My windows are restrained obviously using the force constant in the mdp
file. The trajectories that I have viewed are those of the individual
biased sampling windows. I have not put on the unbiased simulations yet.
There is also the following issue: The simulations involve two identical
molecules containing hydrocarbon chains. I calculate the PMF to take a
specific hydrocarbon chain of one molecule out of a specific site on the
neighbouring molecule. When this guest chain goes out, other chains can
go in (intramolecular or intermolecular). Will this affect the profile?
Gavin
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