From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Feb 07 2005 - 11:33:00 CST
Hello,
The clue here is the dihedrals entry. This does not suggest atoms on top
of each other, rather that some dihedral has been defined incorrectly
in the psf file.
Regards
Brian
On Mon, 7 Feb 2005, Hemant Kushwaha wrote:
> Dear all,
>
> While running NAMD simulation in gas phase we have been facing the
> following problem:
>
> Info: Entering startup phase 8 with 2374 kB of memory in use.
> Info: Finished startup with 2639 kB of memory in use.
> TCL: Minimizing for 100 steps
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP TOTAL2
> TOTAL3 TEMPAVG
>
> ENERGY: 0 30.0566 8.6178 -99999999.9999
> 0.0000 -31.6645 13.8172 0.0000
> 0.0000 0.0000 -99999999.9999 0.0000
> -99999999.9999 -99999999.9999 0.0000
>
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
>
> We loaded the *.pdb strututre in tinker and found no overlap in atoms.
> Can anybody help us in finding out the solution to this problem.
>
> Thanks in advance
>
> Regards
> Hemant R. Khushwaha
> Arunabhiram Chutia
>
************************************************
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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