From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Apr 14 2005 - 18:28:42 CDT
While the cell dimensions might have been contributing to the overall
problem. The root cause is an incorrect description (placement) of atoms.
The dihedral energy is the clue in this case.
I would double check the psfgen portion of your preparation and then
start minization of seperate sections of your system if nothing obvious
sticks out.
Brian
On Thu, 14 Apr 2005, Stern, Julie wrote:
> I did check that and fixed the problem. I had different dimensions in the
> .incprd file than I did in the config file, but I made them the same. And
> the problem still occurred.
>
> -----Original Message-----
> From: Pijush Ghosh
> To: Stern, Julie
> Sent: 4/14/2005 5:48 PM
> Subject: Re: namd-l: minimization problem
>
> Julie
> i dont know if you have got my earlier message, but yes seeing your
> error message i have a kind of feelings that your system is turning
> unstable and one reason could be inaccurate cell dimension.
> ----- Original Message -----
> From: "Stern, Julie" <jvstern_at_bnl.gov>
> To: <namd-l_at_ks.uiuc.edu>
> Sent: Thursday, April 14, 2005 3:26 PM
> Subject: RE: namd-l: minimization problem
>
>
> > Here are the energies:
> >
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP
> > ELECT VDW BOUNDARY MISC
> KINETIC
> > TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG
> > PRESSURE GPRESSURE VOLUME PRESSAVG
> GPRESSAVG
> >
> > ENERGY: 0 472.7316 49.3810 -99999999.9999
> > 0.0000
> > 16167.5620 99999999.9999 0.0000 0.0000
> 0.0000
> > -99999999.9999 0.0000 -99999999.9999 -99999999.9999
> 0.0000
> > -99999999.9999 -99999999.9999 61866.4212 -99999999.9999
> -99999999.9999
> >
> > INITIAL STEP: 1e-06
> > GRADIENT TOLERANCE: nan
> >
> >
> >
> > -----Original Message-----
> > From: Brian Bennion
> > To: Stern, Julie
> > Sent: 4/14/2005 4:12 PM
> > Subject: Re: namd-l: minimization problem
> >
> >
> > Can you give us some more information? Like say, what are the
> energies
> > before this step is printed in the log file?
> >
> >
> >
> > On Thu, 14 Apr 2005, Stern, Julie wrote:
> >
> >> What does it mean if during minimization is says:
> >> INITIAL STEP: 1e-06
> >> GRADIENT TOLERANCE: nan
> >>
> >> and then just sits there. How do I fix this?
> >>
> >> Thanks.
> >>
> >> --Julie
> >>
> >
> > ************************************************
> > Brian Bennion, Ph.D.
> > Bioscience Directorate
> > 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.
Bioscience Directorate
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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