[gmx-users] NMR Structure determination
spoel at xray.bmc.uu.se
Thu Dec 2 20:50:46 CET 2004
On Thu, 2004-12-02 at 19:07 +0100, Wolfram Gronwald wrote:
> >>> spoel at xray.bmc.uu.se 12/01/04 10:07 AM >>>
> On Wed, 2004-12-01 at 09:27 +0100, Wolfram Gronwald wrote:
> > Hi,
> > I am new to GROMACS and have the following question. Is it suited for
> > standard Protein NMR structure calculation starting from an extended
> > strand and if yes are there .mdp parameterfiles available to do so?
> Works fine. Just take care that you turn on distance restraints.
> > Thanks a lot
> > Wolfram
> Thanks for your answer this sounds good, but what parameters should I
> use? Do you have a set for NMR structure determination? In the examples
> I found parameters for doing MD at a constant temperature in a box of
> water, but what I probably need is a simulated annealing run starting at
> e.g. 2000 K and then slowly cooling down to room temperature followed by
> a final energy minimization (at least this is what I usually do when
> using X-Plor).
Simulated annealing is trivial too, just two parameters in the mdp file.
You can also have separate temperatures for protein and solvent.
How big is the protein? Do you already have starting structures?
> Thanks a lot
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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://xray.bmc.uu.se/~spoel
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