[gmx-users] Very large fluctuations in dg/dl
gmx3 at hotmail.com
Tue May 8 13:58:55 CEST 2007
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
>From: Patrick Fuchs <Patrick.Fuchs at ebgm.jussieu.fr>
>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] 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.
>On Tue, 8 May 2007, Berk Hess wrote:
>>>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>>>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] Very large fluctuations in dg/dl
>>>Date: Tue, 8 May 2007 06:39:50 +0200
>>>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
>>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)
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