Re: Parameter/topology repository

From: Jim Phillips (
Date: Fri Nov 07 2003 - 11:05:11 CST


This sounds like a good idea to me. I'd like start with a lightweight
solution and seeing how things evolve by using the NAMD Wiki at to create these pages, either
posting the entries directly or linking them from your own web server.
There isn't a security model, but all revisions are logged and appear on
the RecentChanges page. Sending these entries to NAMD-L would result in
them being permanently archived as well.


On Fri, 7 Nov 2003, Jan Saam wrote:

> Dear fellow NAMDers,
> I would like to propose a repository for parameter and topology files of
> non standard components. I think this would be very helpful to many MD
> people as determining your own top/par set for your molecule can be very
> tedious and nobody likes to reinvent the wheel.
> My suggestion is that the NAMD developers would maintain a little
> database into which we could post our files that also contains entries
> concerning the method how one gained the parameters (combination of
> existing params, QM simulations, etc.) and the publication that you
> would like to be cited in case somebody uses your parameters.
> I would post three or four molecules.
> What do others think about it?
> Jan
> Jan Saam
> Humboldt-Universität Berlin
> Medizinische Fakultät (Charité)
> Institute for Biochemisty
> Monbijoustr. 2
> 10117 Berlin
> Germany
> phone: +49 30 450 528 449
> mail:

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