On Thu, Nov 03, 2011, Daniel Roe wrote:
> > 2. Is it physically reasonable to use NMR-type restraints during an LMOD
> > simulation, or can that lead to non-physical results?
>
> This I don't really have experience with but I can try to offer an
> educated guess. It probably depends on what exactly you're restraining
> and how you're restraining it. In Sander I'm pretty sure the NMR
> restraints aren't applied during the LMOD procedure itself, but in
> between calls to the LMOD routine (others please correct me if I'm
> wrong).
I think you are wrong: NMR restraints are just a part of the energy function,
included every time force() is called. The LMOD driver doesn't know or care
what kind of energy function is being used, but just calls force() when it
needs energies or derivatives. I've not done NMR refinements myself with
LMOD, but things ought to be fine.
...dac
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Received on Fri Nov 04 2011 - 07:30:04 PDT
