Thank you very much for the insight!
~Sarah
On Fri, Nov 4, 2011 at 9:20 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 15:00:03 PDT
