All,
I'm trying to figure out how to use tabulated nonbonded interactions
in GROMACS in conjunction with free energy calculations. While the
documentation addresses both separately, I am somewhat confused about
what would happen if I try to use both simultaneously. In particular,
I'm looking at the discussion of user-defined potentials on page 126
of the 3.3 manual. If I set up a table defining f(rij), g(rij), and
h(rij) as discussed their, plus their derivatives, can I still use the
free energy code?
For example, what if I have a topology file that has full charges on
some molecule in the A state, but zero charges in the B state?
Usually, with the free energy code, the potential energy would be
V=(1-lambda)*V_A+lambda*V_B. However, if I use tabulated nonbonded
interactions, the electrostatic term is qi*qj/4pi*eps0*f(rij); I
assume this means the package will use a *particular* qi and qj (i.e.,
for the A state)?
I'm asking all this because my *goal* is to be able to do free energy
calculations using the WCA separation for LJ. I understand it's
possible to implement the WCA separation using tabulated nonbonded
interactions (at least, there's an e-mail on the list suggesting this)
but it's unclear to me whether doing so would make it impossible for
me to simultaneously do free energy calculations. I'm guessing the
answer is yes -- one can't use tabulated nonbonded interactions and
free energy simultaneously. Can anyone confirm?
Thanks,
David
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