[gmx-users] free energy calculations in charged systems
gmx3 at hotmail.com
Wed Nov 21 09:23:52 CET 2007
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.
>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] free energy calculations in charged systems
>Date: Wed, 21 Nov 2007 09:15:36 +0100
>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.
>Maik Goette, Dipl. Biol.
>Max Planck Institute for Biophysical Chemistry
>Theoretical & computational biophysics department
>Am Fassberg 11
>Tel. : ++49 551 201 2310
>Fax : ++49 551 201 2302
>Email : mgoette[at]mpi-bpc.mpg.de
>WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>Argyrios Karatrantos wrote:
>>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.
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