[gmx-users] Free energy, frozen atoms and exclusions

Ignacio Fernández Galván jellby at yahoo.com
Mon Sep 11 17:14:24 CEST 2006

--- Berk Hess <gmx3 at hotmail.com> wrote:

> >Is there something I'm missing? A bug/feature in the code? A
> >limitation?
> If you are using PME, the mesh contribution is not excluded when
> using energygrp_excl, grompp should give you a warning about this.
> Adding all the pairs as exclusions solves this problem.

Thanks. Would that account for such a large difference, considering
it's a neutral molecule (and at lambda=1, with no partial charges)?

Well... since it's the derivative, and that means the free energy
change from lambda=0 to lambda=1... yes that could be it. Is this
mentioned in the manual? 'Cause I read about the [exclusions] section
and it gives the advice to use energygrp_excl, but doesn't warn about

Would normal Ewald or reaction field work as (I) expected? I guess I
will keep using PME anyway, if it's as easy as adding the [exclusions].

> But why do you want to freeze the methonal?
> Things would be much easier with a free methanol.

At the moment this is only a test. I need the method to work for
arbitrary molecules for which there are no force field parameters, only
LJ. The atomic charges and intramolecular contributions I get them from
other QM/MM calculations. I also need to compare with other rigid-body
simulations. I'm not saying this is the best way to calculate free
energies, but it's the way I need now :)

Thanks a lot for the reply!

PS. The manual mentions using "no" for "comm_mode", but grompp prefers
"none" instead.

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