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
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
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
difficult.
-Dan
On Thursday, January 6, 2011, case <case.biomaps.rutgers.edu> 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
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Jan 06 2011 - 07:00:02 PST
