[gmx-users] Parameters for PB calculation with Delphi from Gromacs data

[Marco Ceruso]

Hi;
If you use Delphi use the PARSE vdw radii set (J. Phys. Chem. 98, 1978-1988
(1994)). For the charges you can keep the OPLS-AA charges.
Marco  
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Marc Baaden
> Sent: Sunday, October 10, 2004 4:49 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Parameters for PB calculation with 
> Delphi from Gromacs data
> 
> 
> Hi,
> 
> I am currently carrying out some Poisson-Boltzmann 
> calculations with Delphi, on the basis of MD snapshots 
> obtained with Gromacs. I wonder what parameter set (charges & 
> radii) would be appropriate for Delphi.
> Should one "simply" take the precise charges as used in the 
> MD simulation, and eventually the VDW-parameter derived 
> atomic radii, or is there some other magic involved to obtain 
> reasonable results ?
> 
> What are people's experience, and would users be willing to 
> share their favorite parameter set ?
> 
> In particular I wonder whether one would need to have 
> different specific Delphi parameters depening on the 
> forcefield used (ffgmx vs ffG43xx vs
> oplsaa) ?
> 
> Or maybe it is more appropriate to use MEAD, as some Gromacs 
> tools allow to write corresponding input structures ?
> 
> Any clarification or (Gromacs related/specific) litterature 
> reference is welcome.
> 
> Thanks in advance,
>   Marc
> 
> --
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
>  FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
> 
> 
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