[gmx-users] Free Energy Calculations in Gromacs

HANNIBAL LECTER hanniballecter13 at gmail.com
Sat Apr 20 22:04:38 CEST 2013


I am trying to perform expanded ensemble simulations between 2 states A
(lambda=0) and B (lambda =1) with 6 intermediate lambda values.

In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
interactions, the charges, the bond, angle and dihedral constants are a
multiple of the similar terms of State A.

It's not quite clear to me (going through the archives of the gmx-users
mailing list how to perform these calculations. One way to do this, is to
use a single topology file in which the charges and the other terms are
specified for both states A and B. However, it is not clear as to how
should I scale the epsilons in the topology file. (My atoms are not mutated
in state B. They are the same atoms with scaled epsilons.)

Secondly, since I have the topology files for states A and B, is there a
way I could perform the simulations (any particular way in grompp) where
both the topology files can be preprocessed designating the end states and
using the mdp options, the simulations corresponding to the intermediate
lambda values performed??

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