RE: minimization problem - "Bad global exclusion count, possible error!"

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 30 2004 - 10:09:19 CST

Hi,

>From the log file provided no periodic boundary conditions were
employed...if I remember right.

Brian

On Thu, 29 Jan 2004, Harindar Keer wrote:

> Hi,
>
> Check if some bonds in complex are crossing the periodic cell
> boundary, fixing the complex such that nothing crosses the boundary
> before minimization might help. Although I am not sure but reason might
> lie in way interactions are calculated under boundary conditions, as one
> atom leaves one side of cell it appears in the cell from opposite side.
> Being part of same bond but now more than cutoff distance away might
> cause the warning.
> Please correct if someone knows the reason.
>
> Regards,
>
>
> On Thu, 2004-01-29 at 19:20, Frances Leung wrote:
> > Hello,
> >
> > I think it's a little different for my case. Previously I successfully
> > minimized my protein complex. I even finished equilibrating it.
> > However, the process took so long and I expected the SMD would take even
> > longer and due to time constraints, I decided to do just half of the
> > protein (the protein has two chains, now I'm trying to do simulation on
> > just one of the chains to save time since both chains are essentially
> > identical). I didn't get warnings like these when I was minimizing the
> > complete protein complex, but now that I'm doing just half of it, I get
> > problems. I wonder what I need to do to get through the minimization
> > part by simulating just one chain?
> >
> > Frances
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> > Behalf Of Brian Bennion
> > Sent: Thursday, January 29, 2004 3:47 PM
> > To: Uday Chippada
> > Cc: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: minimization problem - "Bad global exclusion count,
> > possible error!"
> >
> > Hello,
> >
> > After having a problem in my topology file cause the same error I would
> > highly advise looking at the HYP residue you created and make sure the
> > bonding is corect. Just checking the psf file in vmd didn't catch my
> > mistake. It sounds like a bond is actually missing in your case.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, 29 Jan 2004, Uday Chippada wrote:
> >
> > > Hi,
> > >
> > > I am getting the same error too. Also in the end the error that is
> > > shown is something like
> > >
> > > ERROR: Constraint failure in RATTLE algorithm for atom 231!
> > > ERROR: Constraint failure; simulation has become unstable.
> > > ERROR: Exiting prematurely.
> > >
> > > I recieved the same error while working with the 1QSU molecule which
> > > had a HYP residue, for which there was no entries in topology file or
> > > the parameter file. So I included these values for HYP, and got the
> > > error. So I attributed it to the HYP residue.
> > >
> > > But when I tried for the 1A3J chain from the protein data bank, I
> > still
> > > got the same error, this one has just PRO and GLY residues.
> > >
> > > I read in some previous messages that it could be because of the
> > sphere
> > > radius, but I checked it and even varied it drastically to no avail.
> > >
> > > When I try the 1UBQ given in the tutorial on the NAMD site, it works
> > > fine.
> > >
> > > Any help would be greatly appreciated. Thank you
> > > Sincerely
> > > Uday Chippada.
> > >
> > > > Hi,
> > > >
> > > > I'm trying to do the minimization for a protein complex and keep
> > > getting
> > > > these warnings:
> > > >
> > > > Warning: Bad global exclusion count, possible error!
> > > > Warning: Increasing cutoff during minimization may avoid this.
> > > >
> > > > Does anyone know what this means? The log file is attached.
> > > >
> > > > Regards,
> > > >
> > > > Frances
> > > >
> > >
> > >
> > >
> >
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

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