Hi All,
Just my 3c. If we plan to implement a new restart format, and NETCDF would
be cool I think we should try to do this properly and make 'real' restarts.
That is we store all of the various settings and things such as the random
number generator state etc as well as all the coordinates, velocities etc in
machine precision such that one really can do 'proper' restarts.
Perhaps we should consider this an action item for discussion at the
developers meeting.
All the best
Ross
> -----Original Message-----
> From: B. Lachele Foley [mailto:lfoley.uga.edu]
> Sent: Thursday, January 06, 2011 6:31 AM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] netcdf restart files?
>
> 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
> >
> >
> > _______________________________________________
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> > 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
>
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>
>
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Received on Thu Jan 06 2011 - 10:00:04 PST
