Re: [AMBER-Developers] netcdf restart files?

From: B. Lachele Foley <>
Date: Thu, 6 Jan 2011 14:30:34 +0000

We think it would be great. We're getting to the point now that we occasionally have trajectories with stars. It isn't feasible to use iwrap because iwrap will "break apart" a non-bound complex. So, if a really big & long simulation crashes, it can't be restarted.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Daniel Roe []
Sent: Thursday, January 06, 2011 8:57 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] netcdf restart files?

I have a lot of experience with the Netcdf format and can implement a
restart file if people think it's a good idea. I think it's a great
idea and I feel that since there is already an amber netcdf traj
format getting programs like vmd to support it shouldn't be too


On Thursday, January 6, 2011, case <> wrote:
> On Wed, Jan 05, 2011, B. Lachele Foley wrote:
>> Has there been discussion of making it possible to read and write
>> netcdf-formatted restart files? If not, can I start that discussion?
>> If so, is it planned or already available?
> a. We already have an "unformatted" restart file option, which might be
> fine since the data inside a restart file is very simple, and might not
> need the complexity of a netcdf wrapper. I couple of revisions ago, this
> option was disabled, but that was probably a bad decision. I have made
> repeated requests for developers to turn it back on and try things out,
> since I don't think it is broken, just disabled. So far, there have not
> been any takers, which may reflect how much influence I really have....
> b. There are advantages to going to a more elaborate netcdf format, since
> libraries for reading/writing these files are now routinely included in
> sander, ptraj and NAB. (We were reluctant to do this earlier, since netcdf
> did not compile cleanly everywhere.) If someone wants to work on this, that
> is fine as well.
> I think this is an important thing to do, since it would eliminate (to some
> extent) the need to set iwrap in sander/pmemd and remove the dreaded ***
> problem. It would also remove the small amount of noise that occurs on
> restarts due to truncation of precision in current (formatted) restart files.
> The downside (and the reason we turned off binary restarts in the first place)
> is that increases the complexity of everything: having two different restart
> formats means that every program that interfaces with these needs to know
> about both options. This includes not only things we control (ptraj, mm-pbsa,
> NAB....) but programs written by others (VMD, Chimera, ....).
> But I still think it is worth doing.
> ...dac
> _______________________________________________
> AMBER-Developers mailing list

Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
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Received on Thu Jan 06 2011 - 07:00:02 PST
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