[gmx-users] Regarding relative free energy calculation
bipinelmat at gmail.com
Wed Dec 11 18:16:45 CET 2013
I am trying to calculate relative free energies of hydration between two
similar molecules. I want to do the following things:
(1) Totally remove the VDW and Coulomb interactions of few atoms (remove
their interaction with all atoms).
(2) Transform the Coulomb term (partial charge) of few atoms to a certain
value (such that this value will be the one relevant for the interactions
with all the other atoms).
If I understand correctly the (1) transformation can be implemented by
turning the charges to zero in state B and further changing it to DUM atoms
by another transformation.
Could you please advise if the (2) option can be implemented through
Gromacs free energy mdp options?
Thanks in advance.
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