Dear Amber users,
I have some questions about manual editing prmtop files for free energy
calculations. In prmtop file exists some lines with flags:
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
%FLAG
LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
My question is if I change approprietely Lennard_Jones coefficients in
these lines, do i get same free energy of turning off van der Waals for
solvent in solution, as in calculation with dummy atoms?
Thank you for answers in advance.
Audrius
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Received on Fri May 25 2012 - 04:30:03 PDT
