[gmx-users] Free energy for charged molecules with PME

Berk Hess gmx3 at hotmail.com
Fri Feb 22 09:55:46 CET 2008

> Date: Thu, 21 Feb 2008 16:32:45 -0700
> From: anirban.mudi at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Free energy for charged molecules with PME
> dear gmx users
> Any rigorous approach available currently to solve the problems mentioned in the link below ?
> http://www.mail-archive.com/gmx-users@gromacs.org/msg03792.html
> Is gromacs 4.0 going to have a way to deal with them ?
> Sorry to bother if a solution has been posted already and I have missed it.

There is no "technical" solution possible for this problem.

You always need a complete thermodynamic cycle.
So if you make a charge dissappear it needs to appear somewhere else.
One can simulate both these processes separately. But in both processes
there is the background charge issue. If your both systems have a spatially
homogeneous dielectric behavior, the background charge does not affect
the results. When this is not the case, one can not simulate the processes
in this way. One way of doing it would be to make the charge dissappear
in one spot and make it appear in another spot in the same system.


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