[gmx-users] atom types @ bonded parameters

David van der Spoel spoel at xray.bmc.uu.se
Fri May 18 16:52:06 CEST 2007

Francesco Pietra wrote:
> New to the list, aimed at installing gromacs on Linux
> Debian amd64 dual-core-opterons for parallel
> execution, I would appreciate indications where (not
> having yet installed gromacs) to find: 
> ---Atom types list.
> ---Bonded parameters list.
> ---Any tool to generate new bonded parameters.

> I am well equipped of QM suites and have also some
> experience with classical MD. My problem was always
> lack of bonded parameters and atom types that I need
> for my studies.

If you kow your QM a frequency calculation of your molecule should give 
you force constants and optimization the equilibrium distances and 
angles. only problem is torsion parameters. for these you have to read 
the appropriate force field papers.

> Thanks
> francesco pietra
> (This is a project of mine of long date, and I also
> had exchange of emails with the Debian gromacs
> maintainer; though, it is only now that I have the
> time to try to start).
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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