Re: "GRADIENT TOLERANCE: nan", Why?

From: Zhong Wenyu (wyzhong78_at_163.com)
Date: Thu Jun 03 2004 - 09:02:01 CDT

Hi, Brian.
Thanks for your help. I found out the reason, the coordinate guessed by psfgen made some angles of 0 degree.

----- Original Message -----
From: "Brian Bennion" <brian_at_youkai.llnl.gov>
Cc: "NAMD" <namd-l_at_ks.uiuc.edu>
Sent: Thursday, June 03, 2004 5:04 AM
Subject: Re: namd-l: "GRADIENT TOLERANCE: nan", Why?

>
> Hello,
>
> This error is very suggestive of incorrectly built system box. The atoms
> are nearly on top of each other according to the VDW entry, and bonds seem
> to be cut in half, making angle energies off the scale.
>
> Recheck your box size and send your config file with psf and pdb files if
> you need more help.
>
> Brian
>
>
> On Wed, 2 Jun 2004, Zhong Wenyu wrote:
>
> > Hi.
> > I have constructed a system contains lipid and DNA and carbon nanotube.The parameters files I used are par_all27_prot_lipid.inp and par_all27_na.inp. I meet some problems in minmization.
> >
> > TCL: Minimizing for 1200 steps
> > PRESSURE: 0 nan nan nan nan nan nan nan nan nan
> > GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
> > ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
> >
> > ENERGY: 0 126435.5317 -99999999.9999 16158.4504 246.0499 -690784.5080 99999999.9999 0.0000 0.0000 0.0000 -99999999.9999 0.0000 -99999999.9999 -99999999.9999 0.0000 -99999999.9999 -99999999.9999 2906800.0000 -99999999.9999 -99999999.9999
> >
> > INITIAL STEP: 1e-06
> > GRADIENT TOLERANCE: nan
> >
> > Then the computation hold on, neither stop nor continue work.
> > Anyone could help me?
> > Best regards.
> >
> > Wenyu Zhong
>
> *****************************************************************
> **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 **
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