[gmx-users] PMF in vacuum

[Eudes Fileti]

Hi gmx-users,
I'm trying to simulate a umbrella sampling PMF between two benzene
molecules
in vacuum. My protocol is working fine, my histograms have good overlap and
the curves I have got are quite reasonable.

However I have noticed that some options in my .mdp file can significantly
change
the depth of the well. Also the curves can not go to zero at long distances.
For example, if I use PBC I get a reasonably good value for the minimum of
the PMF
but from a certain separation it starts to increase slightly in a linear
fashion
instead of going to zero. On the other hand, if I make pbc = no, I get an
acceptable curve,
with the PMF going to zero, but with the minimum too high.

Someone could give me any tips on the best set of parameters to calculate
this PMF in a vacuum?
bests
eef
_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4996-0196
http://fileti.ufabc.edu.br
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