[gmx-users] GROMACS and XML

[Anton Feenstra]

David van der Spoel wrote:
> 
> 1. Molecule description
> 2. Force field description
> 3. Simulation parameters
> 
> My current way of thinking is to create 3 DTDs which then are combined
> into one master DTD. One could also conceive having quantum chemical
> information instead of 2 (i.e. basis sets).

Just as a small note: I would suggest the possibility of *adding* QC
information in stead of replacing the ff by QC. That opens the way to
a QM/MM approach, similar to what Gerrit is already implementing.

> A practical  drawback of separating 1 and 2 is that a certain amount of
> information has to be duplicated. E.g. in 1 we would specify that there is
> a bond between N and Ca in an Ala residue, this information would also
> have to be incorporated in 2 in some way, to be able to add the
> appropriate bond length and force constants.

But it would also allow a quite rigorous error-checking, i.e. wheter
all bonds defined in the topology actually are defined parameters in
the forcefield description as well.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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