[gmx-users] Free energy for charged molecules

Ignacio Fernández Galván jellby at yahoo.com
Fri Sep 22 09:37:47 CEST 2006

--- David Mobley <dmobley at gmail.com> wrote:

> > Is there any "gotcha" with charged molecules?
> In my opinion, yes. This has been discussed some on the list before
> so
> I encourage you to search the archives. The basic problem is that,
> when using PME (as you are) the system must be net neutral. When you
> turn off or on a charge in your system, you are necessarily making
> the
> system charged. Most PME codes are actually designed to be able to
> handle this (in the sense of not exploding) by introducing a uniform
> neutralizing background charge to enforce neutrality.

Thanks for your reply. I had actually search the archives but didn't
find any clear answer (maybe the search was not so good)... You mention
this is a problem with PME, would plain Ewald or even Reaction-Field be
less problematic in this case? And how large do you estimate the cutoff
should be to give reasonable results? My system is a small molecule
(~20 atoms) in water, so I can afford building boxes with a lot of

Ignacio Fernández Galván

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