From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jan 04 2005 - 10:46:40 CST
Have you looked at the namdwiki page
http://www.ks.uiuc.edu/Research/namd/wiki/?NamdTroubleshooting
and excluded any of these possibilities?
Brian
On Mon, 3 Jan 2005, bora erdemli wrote:
> Dear All;
>
> I need help about the following error occured during
> simulation.
>
> Processor 0 Exiting: Called CmiAbort
>
> Reason: BUG ALERT: Stray PME grid charges
> detected!
>
> BUG ALERT: NAMD has detected a bug. Please notify
> namd_at_ks.uiuc.edu.
>
> req_handle_abort called
> Fatal error on PE 0> BUG ALERT: Stray PME grid
> charges
> detected!
>
> BUG ALERT: NAMD has detected a bug. Please notify
> namd_at_ks.uiuc.edu.
>
> I could visualize my system and everything seems to be
> ok . I have some free charges around my system which I
> did put them by using VMD autoionize plug-in in order
> to neutralize the system. I made 10000 minimization by
> using usual NAMD procedure no simulated annealing or
> such modification.
>
>
> --- Ioana Cozmuta <ioana73_at_gmail.com> wrote:
>
> > Did you vizualize your trajectory? Do you have free
> > charges
> > (counterions) around your system? What system are
> > you looking at? What
> > was your equilibration procedure? Do you see the
> > system splitting
> >
> > If you give more information I might be able to help
> > if none else has
> > a better idea.
> >
> > Ioana
> >
> >
> > --
> > Ioana Cozmuta, Ph.D.
> > Eloret Corporation
> > NASA Ames Research Center
> > http://people.nas.nasa.gov/~ioana/
> > w (650) 604-0993, h (408) 732-1399
> > On Thu, 23 Dec 2004 23:06:32 -0800 (PST), bora
> > erdemli
> > <boraerdemli_at_yahoo.com> wrote:
> > >
> > > Dear All;
> > >
> > > After almost 2 ns simulation , I faced with the
> > > following error and my simulation was stopped.
> > > What could be the reason?
> > >
> > > best regards....
> > >
> > > ------------ Processor 0 Exiting: Called CmiAbort
> > > ------------
> > > Reason: BUG ALERT: Stray PME grid charges
> > detected!
> > >
> > > BUG ALERT: NAMD has detected a bug. Please notify
> > > namd_at_ks.uiuc.edu.
> > >
> > > req_handle_abort called
> > > Fatal error on PE 0> BUG ALERT: Stray PME grid
> > charges
> > > detected!
> > >
> > > BUG ALERT: NAMD has detected a bug. Please notify
> > > namd_at_ks.uiuc.edu.
> > >
> > > =====
> > > Sabri Bora Erdemli
> > > Koc University
> > > Computational Science and Engineering
> > > Research and Teaching Asistant
> > > Koc Universitesi pk.218 34550
> > > sariyer Istanbul/TURKEY
> > > tel no: 02123381736
> > > 05326512523
> > >
> > >
> > > __________________________________
> > > Do you Yahoo!?
> > > Yahoo! Mail - You care about security. So do we.
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> > >
> >
>
>
> =====
> Sabri Bora Erdemli
> Koc University
> Computational Science and Engineering
> Research and Teaching Asistant
> Koc Universitesi pk.218 34550
> sariyer Istanbul/TURKEY
> tel no: 02123381736
> 05326512523
>
>
>
>
>
>
> __________________________________
> Do you Yahoo!?
> Send a seasonal email greeting and help others. Do good.
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>
*****************************************************************
**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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