[gmx-users] Doubt in free energy calculation options

bipin singh bipinelmat at gmail.com
Sat Dec 14 09:57:00 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?. And  what should be the "coupl-intramol"
value to be used during these transformations (I do not want to decouple
solute-solvent interaction during these transformations).

Thanks in advance.


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

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