Hi Berk,
I just wanted a confirmation because it's a critical aspect. Beyond the
debate between PME and RF, I always read it was important to be consistent
with the (early) force field parameterization when deriving new parameters.
Even if it does not make any difference for solvation free energy, I
imagine this can give some differences on other properties (e.g. heat of
vaporization...), or if you want your new parameters to be consistent with
the remaining of the force field.
Ciao,
Patrick
On Tue, 8 May 2007, Berk Hess wrote:
Hi,
I don't understand why you ask this.
Or didn't you read or understand my previous answer?
Reaction-field and PME give exactly the same solvation free-energies,
so you can just as well derive parameters for the GROMOS force-field
using PME.
Berk.
From: Patrick Fuchs <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] Very large fluctuations in dg/dl
Date: Tue, 8 May 2007 12:45:32 +0200 (CEST)
Hi Berk and Tsjerk,
sounds reassuring since the last version of the GROMOS force field (G53a5
and a6) has been parametrized to reproduce DGsol using reaction field.
But, you agree Berk that when you want to calculate the solvation free
energy in the "GROMOS philosophy" (e.g. for reproducing or computing new
parameters), you have to use RF even if energy conservation might not
be as good as with PME?
Thanks for your answers and your interest in the thread.
Cheers,
Patrick
On Tue, 8 May 2007, Berk Hess wrote:
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: Re: [gmx-users] Very large fluctuations in dg/dl
Date: Tue, 8 May 2007 06:39:50 +0200
Hi Berk,
Just a question relating to your reply (should be a new thread
maybe...). The Gromos force fields were parameterized (for use) with
cutoff/RF. PME is of course better for energy conservation, but the
inclusion of the interactions beyond the cut-off may give rise to
deviant behaviour from the force field. Could you enlighten me on this
issue?
Thanks,
Tsjerk
Luckily it does not.
And PME is not only better for energy conservation, but also captures
long-range interaction, which for instance leads to more stable proteins.
I have compared solvation free energies for G53A6 with reaction-field
and PME and found no differences:
B. Hess and N. van der Vegt
Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic
Comparison of Biomolecular Force Fields and Water Models
J. Phys. Chem. B 110, 17616 (2006)
http://dx.doi.org/10.1021/jp0641029
Berk.
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