[gmx-users] PRODRG

[Daan van Aalten]

Peter

You are confusing topology with conformation. For each bond between a
pair of atoms there is a choice of several hundreds of bond types, which
are associated with a) specific force constants and b) specific
equilibrium values (i.e. bond lengths). Same for bond angles.
You can minimize coordinates, but the topology stays the same.

Writing out a G96 FF topology is probably only a day's work if I can have
a full day's use of a G96 FF guru for advice and testing - and of course
everyone is busy!

cheers

Daan

On Wed, 19 May 2004, Peter Zoon wrote:

> >The atom types aren't the problem but the manual conversion of
> >bonds/angles/dihedrals to G96 types. IMHO this may be intricate in
> >some cases. I guess it would be very nice to have a G96 topology
> >automatically generated by PRODRG, the GMX force field seems to be
> >considered rather outdated even by the Gromacs crew themselves.
>
> That doesn't matter right?
> If you do a minimization (after you changed to the right atom-types),
> the system will just equilibrate and you will reach the right
> topology automatically.
>
> Or am I making a reasoning error here?
>
> Peter
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Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
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