[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.
> 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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