[gmx-users] NMR Structure determination

Wolfram Gronwald wolfram.gronwald at biologie.uni-regensburg.de
Thu Dec 2 19:07:15 CET 2004

>>> 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).

Thanks a lot

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