[gmx-users] Parameters for PB calculation with Delphi from Gromacs data
mceruso at physbio.mssm.edu
Sun Oct 10 23:17:13 CEST 2004
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.
> -----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
> 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,
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users