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