First of all, PME is always the best option.
If PME can not do it, cut-off or reaction-field electrostatics can surely
not do it.
You have given a very short description of the problem.
I don't understand what you want to do exactly.
It is very difficult to change the net charge of your system,
also in most cases there there will not be an experiment to compare to.
You can get free energies when the net charge does not change,
for instance for simutaneously discharging ions and counterions.
But there I don't see how the end state could be a realistic system.
Also it could be difficult to sample.
But the capabilities of Gromacs are not the issue here.
Berk.
From: Maik Goette <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] free energy calculations in charged systems
Date: Wed, 21 Nov 2007 09:15:36 +0100
Hi
Cant' give you a sound answer, but from what I heard from talking to people
in the field, PME can't handle that properly. Maybe Cut-Off/Reaction-Field
should be the long-range treatment of choice. Still, I don't know, if there
may occur problems with that.
Maybe David (both) or Berk have some more sound comments on that.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Argyrios Karatrantos wrote:
Hi all,
i am working in polyelectrolyte solutions, and i would like to calculate
the free energy for the polyectrolyte system (charged) to change to a
neutral (non-charged) system.
The question is if it feasible to use the PME electrostatics in gromacs
for the above
free-energy calculation.
thanks
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