On Thu, Jan 6, 2011 at 9:30 AM, B. Lachele Foley <lfoley.uga.edu> wrote:
> 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.
>
There is one thing you can do: in the prmtop are sections called
SOLVENT_POINTERS and ATOMS_PER_MOLECULE. If you reduce NSPM by 1 and
combine the unbound complex into a single molecule, iwrap will not image
them separately. This would probably be a fairly straightforward addition
to your prmtop utility.
That said, I second the binary restart file movement. I would think that
perhaps visualization programs that already support Amber netcdf files would
already support binary restarts and netcdf seems to build fairly reliably in
my experience.
All the best,
Jason
> :-) 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
>
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>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 06 2011 - 08:00:03 PST
