AMBER Archive (2007)

Subject: Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!!

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Oct 05 2007 - 22:48:59 CDT

Hi Anthony,

If you can't use iwrap, another option is to use binary trajectory
files. AFAIK, those are not limited by the same field size constraints
as the formatted files. Also, according to the manual, the NetCDF
Binary trajectory files are "smaller, higher precision and
significantly faster to read and write. NetCDF provides for file
portability across architectures, allows for backwards compatible
extensibility of the format and enables the files to be
self-describing. " (p.4)

 So, what I suggest is that you just go back to the last good restart
and, from there on, run your calculations using IOUTFM=1. You may need
to recompile Amber using the -bintraj flag for the 'configure' script.

Gustavo.
P.S. You won't be able to read your trajectory file in a regular
editor (e.g. vi), but ptraj supposedly can handle it just as well as
the regular files.

On 10/5/07, Anthony Cruz <acb15885_at_uprm.edu> wrote:
> Hi Ross,
> How I could do the iwrap for one step???? I need to make one run of only one
> step and then continue the simulation from this point or there is any form of
> doing the iwrap for one steep only ???
> Because I run the part of the simulation that give me the problem (500 ps)
> with the iwrap and the others with out the iwrap and I see a strange behavior
> in the RMSD. Because when I extract the last frame from the mdcrd file (that
> I assume that will be the same as the restart file) and I use the coordinates
> in this file for fix the restart file I dont have the strange behavior in the
> RMSD. See the attach picture. The black is the one that I fix the red is
> with iwrap for 500 ps. If I only run the iwrap for one steep this behavior
> could be fix?
>
>
> Anthony
>
> On Wednesday 26 September 2007 11:51 am, Ross Walker wrote:
> > Hi Anthony,
> >
> > Go back to the previous good restart file and re-run it but in the input
> > file select iwrap=1. This will wrap everything back into the central box
> > and deal with the issue of waters having diffused too far from the central
> > box. 1 step is good enough. Then you can set iwrap=0 again and continue
> > your run. Alternatively you can leave iwrap=1 for your entire run and avoid
> > this simulation but note it can cause issues with calculating RMSD,
> > diffusion constants etc, especially if your solute diffuses out of the
> > central box.
> >
> > Good luck.
> > Ross
> >
> > /\
> > \/
> >
> > |\oss Walker
> > |
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> > > -----Original Message-----
> > > From: owner-amber_at_scripps.edu
> > > [mailto:owner-amber_at_scripps.edu] On Behalf Of Anthony Cruz
> > > Sent: Wednesday, September 26, 2007 07:56
> > > To: amber_at_scripps.edu
> > > Subject: AMBER: Simulation continuation problem. Cant read
> > > restart file!!!!!!
> > >
> > > Hi User:
> > > I have been wotking with a simulation of a heme protein in
> > > water. I decide to
> > > run the simulation in multiple steeps of 500 ps. Right now I
> > > have 116 part
> > > of 500ps (aprox. 60 ns). The problem is that when I re-start
> > > the simulation
> > > to do other 5ns of simulation the simulation stop because one
> > > of the parts
> > > cant read the box or the restart file from the previous part.
> > > When I check
> > > the file I found the some of the coordinate were written as
> > > *. I restart all
> > > the parts again and have the same problem again. How I can
> > > resolve the
> > > problem of the coordinates in the restart file???
> > >
> > > Best regards,
> > > Anthony
> > > --------------------------------------------------------------
> > > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu