[gmx-users] Regarding relative free energy calculation

bipin singh bipinelmat at gmail.com
Wed Dec 11 18:16:45 CET 2013

Dear all,

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.


*--------------------Regards,Bipin Singh*

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