Hi,
In the manual of gromacs, the entropic contribution to the pmf is
emphasized. In my opinion, this contribution is originated from the
rotations of the constrained groups.
However, according to the manual suggestion, "...when calculating a PMF
between two solutes in a solvent, for the purpose of simulating without
solvent, the entropic contribution should be removed." I'm really confused
with this.
If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl-
and many water molecules), I want to calculate the potential of mean force
of NaCl, should I count the contributions from the entropic effects?
According to Hess et al., (2006), JCP, 124: 164509, this effect should
surely be added.
So, any one experienced with similar researches can give me an answer
for this: when should I add the entropic contribution to the pmfs? and, what
the really physical explanation for this effect?
Thanks in advance!
Regards,
zgzhang
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