[gmx-users] Gromacs and DNA ???

[Marc Baaden]

Hi,

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,

Cheers,
  Marc

-- 
 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