[gmx-users] free energy perturbation
giovanni.bussi at gmail.com
Mon Dec 14 16:09:43 CET 2009
I will try the second solution you proposed (which seems more flexible).
So, I should edit the top file (as explained in the "Topologies/File
formats/Topologies for free energy calculations" section of the
manual). And I should NOT use "couple-moltype" anymore, which is just
a shortcut for the standard case of switching a single molecule.
Thanks a lot Berk.
On Mon, Dec 14, 2009 at 3:49 PM, Berk Hess <gmx3 at hotmail.com> wrote:
>> 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
> 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
> 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,
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