Re: [AMBER-Developers] netcdf restart files?

From: Daniel Roe <>
Date: Thu, 6 Jan 2011 08:57:03 -0500

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
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> AMBER-Developers mailing list

Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854
AMBER-Developers mailing list
Received on Thu Jan 06 2011 - 06:00:03 PST
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