On Fri, Apr 26, 2013, Krisztina Feher wrote:
>
> we would like to run a MD with a few NMR derived distance
> restraints. Could this be done with the SA protocolls for NMR structure
> calculation? Or would the non-contrained parts be problematic during
> high T dynamics of SA? Is there any recommended protocoll for such
> partially contrained RMD?
I don't think there is any general answer to your question. You clearly have
to be careful running high-temperature MD if you don't have a lot of
restraints (and you don't want the system to unfold).
Even with lots of NMR restraints, there is no single SA protocol that will
always work. In these "modern" times, you might be better off looking at
replica-exchange techniques (rather than simulated annealing) to find good
structures.
...good luck...dac
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Received on Fri Apr 26 2013 - 17:30:04 PDT
