Re: [AMBER-Developers] NMR restraints and re-imaging

From: Daniel Roe <>
Date: Wed, 8 Nov 2017 15:37:03 -0500

On Wed, Nov 8, 2017 at 2:46 PM, David Cerutti <> wrote:
> 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.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Nov 08 2017 - 13:00:02 PST
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