The cause might be due to non-imaging explicit water or net system
translation
in GB. 1ns isn't very long, though. To say more we would need to know if it
is a
PME or GB run, and if center of mass motion removal was used.
Were initial energies or pressure very high?
Carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Department of Chemistry Fax: (631) 632-1555
SUNY at Stony Brook Web: http://comp.chem.stonybrook.edu/carlos
Stony Brook, NY 11794-3400 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================
----- Original Message -----
From: "jim caldwell" <caldwell_at_heimdal.compchem.ucsf.edu>
To: "Michael Cooney" <mike_at_bmbiris.bmb.uga.edu>
Cc: <amber_at_cgl.ucsf.edu>
Sent: Friday, June 15, 2001 1:54 PM
Subject: Re: coordinate blowup in sander
>
> The only thing you can do is to rerun the calculation,
> this time specify that the coordinate file is saved
> in binary format. However, the presence of "******"
> in the file probably means something else is going
> wrong as well.
>
> jim
>
> On Fri, 15 Jun 2001, Michael Cooney wrote:
>
> > Dear Amber users,
> >
> > In carrying out an MD simulation beyond 1 nsec (1000 psec), I ran into a
> > crippling problem in the mdrestart file, namely that some coordinates
> > "blew up" and registered as ******** (fortran for overflow). The result
is
> > that sander can't use the restart file for further calculations. The job
> > was running on a campus machine and exceeded its cpu time limit, but I
> > don't think this is the real cause of the overflow---the rst file was
> > written before the job terminated. The unexpected character Fortran
> > warning occurs when trying to restart the md run. If needed, I can send
a
> > few sample lines from the rst file.
> >
> > Any help would be greatly appreciated.
> >
> > Thank you,
> >
> > Michael Cooney
> > Dept. of Biochemistry and Molecular Biology
> > The University of Georgia
> > Athens, GA 30602, USA
> >
> >
> >
>
>
> --------------------------------------------------------------------------
--
> James W. Caldwell (voice) 415-476-8603
> Department of Pharmaceutical Chemistry (fax) 415-502-1411
> Mail Stop 0446 (email)
caldwell_at_heimdal.ucsf.edu
> 513 Parnassus Avenue
> University of California
> San Francisco, CA 94143-0446
> --------------------------------------------------------------------------
--
>
Received on Fri Jun 15 2001 - 11:46:36 PDT
