[gmx-users] free energy perturbation

Berk Hess gmx3 at hotmail.com
Mon Dec 14 15:49:25 CET 2009

> From: giovanni.bussi at gmail.com
> Date: Mon, 14 Dec 2009 13:47:37 +0100
> To: gmx-users at gromacs.org
> Subject: [gmx-users] free energy perturbation
> Dear all,
> I am using GROMACS with free-energy perturbation to switch off a
> molecule gradually. If I understand correctly, the parameter
> "couple-moltype" is used to select which molecule to switch off. Is it
> possible to switch off *two* molecules at the same time? (e.g. a
> charged molecule and a neutralizing ion).

I have not implemented this yet.
It would indeed be useful.

> In case not, is there any problem related to the fact that in one of
> the topologies the total charge is not zero?

Yes, this will create problems, because you are then also calculating the cost
of building up a uniform backbground charge, both in case of PME and RF.

Note that free-energies of solvation of ions are huge numbers and are relatively
difficult to determine, both in simulation and in experiment.

There are two way to work around this problem:
Put both molecules together in one moleculetype definition.
Or simply manually set the LJ and charge of the ion to zero in the A or B state topology.


> Thanks a lot,
> Giovanni
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