On Wed, Nov 8, 2017 at 2:46 PM, David Cerutti <dscerutti.gmail.com> wrote:
> I THINK IT'S A BUG FIX:
> The current setup re-images all coordinates, molecule by molecule, relative
> to a single reference frame, then applies the NMR restraints (and any
> bonded interactions) to those coordinates. Bonds are safe, but if an NMR
> restraint applies between two separate molecules, there is a slim chance
> that they will have been re-imaged in a way that suddenly puts an
> additional box length between them. So the proposed change, which would
I'm in the middle of an office move today so I don't have time to look
at this in-depth right now, but I was under the impression that
sander/pmemd only ever image coordinates for output (not internally).
This is why a simulation with restraints will work for an initial run
but sometimes not for the restart. I've got several DNA-stretching
runs where this was in fact the case, unless the code has been
significantly modified since then.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Nov 08 2017 - 13:00:02 PST
