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

Marc Baaden baaden at smplinux.de
Sun Oct 10 22:49:25 CEST 2004


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

Thanks in advance,

 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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