[gmx-users] NMR Structure determination
wolfram.gronwald at biologie.uni-regensburg.de
Fri Dec 3 13:07:29 CET 2004
> Thanks for your answer this sounds good, but what parameters should I
> use? Do you have a set for NMR structure determination? In the
> 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
> e.g. 2000 K and then slowly cooling down to room temperature followed
> 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
it is a small protein of roughly 70 residues in size and I would like to
start from an extended strand.
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