[gmx-users] Gromacs and DNA ???
baaden at smplinux.de
Tue Feb 11 16:27:31 CET 2003
as I have recently taken up a new position in a lab that is deeply involved
in DNA - and I have no personal experience with DNA - I am trying to assess
how useful Gromacs can/could be for us.
I have noted the problems recently discussed on the list with respect to
DNA forcefields implemented in Gromacs.
What I am more interested in right now is whether Gromacs can be used to
analyze existing DNA trajectories (obtained with Amber).
Has anybody got experience with this ?
In particular I wonder:
- how to make Gromacs "understand" my Amber system (eg conversion of
topology, PDB file and trajectory) - in particular with respect to
doing analysis, a "sloppy" way of conversion might be sufficient
- how Gromacs DNA nomenclature works (3"/5", single helix vs double
helix, etc.) and if it is fundamentally different/incompatible with
the Amber one or with NDB format
- whether there is/will be any DNA specific analysis routines in gmx
If anybody has experience with DNA+Gromacs, either in analysis or also
in simulations, I'd be quite interested in your opinion.
Thanks a lot for your input,
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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