Re: [AMBER-Developers] Amber10 REMD with NETCDF trajectory fix

From: Daniel Roe <>
Date: Tue, 10 Feb 2009 10:55:54 -0500

That's probably the best idea. In this case I think that having a bugfix
(that I'm 90% sure is ok) posted for a problem like this is better than
having nothing posted at all. This way if there is some issue with the patch
it will come to light much faster and I can fix it.

Sorry for not catching this sooner.


On Tue, Feb 10, 2009 at 10:20 AM, David A. Case <>wrote:

> On Mon, Feb 09, 2009, Daniel Roe wrote:
> >
> > A while back I had added support in amber11 for writing Netcdf
> trajectories
> > during REMD by adding a replica temperature field to the files. I also
> > updated ptraj so it could read these files. I was under the impression
> that
> > netcdf trajectories with REMD was disabled in Amber10 since the
> trajectories
> > written out have no temperature info, but this turns out not to be the
> case.
> > I am attaching patches for sander and ptraj in Amber10/Ambertools (the
> > latest bugfix versions) that will enable REMD Netcdf support in both. I
> have
> > done some testing, but I would appreciate any error reports as soon as
> > possible. This bug is something that anyone who does a lot of REMD needs
> to
> > know about. I apologize for not catching it earlier.
> Hi Dan:
> It looks like you've run these a lot, and they have been in Amber11 for
> a while. Should I go ahead and post them to the bugfix page?
> ...thanks...dave
> _______________________________________________
> AMBER-Developers mailing list

Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741
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Received on Wed Feb 11 2009 - 01:19:39 PST
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