Re: Value 99999999.9999 during minimization

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Fri Aug 08 2008 - 03:44:12 CDT

Hi Rebeca,

without knowing any details of your system and simulation parameters,
it looks like your structure has some clashes. Maybe you wish to
inspect your system for
atoms being too close to each other.
As the piece of the output you posted shows, the large number is
showing you the
van der Waals energy. But also the bond and the electrostatic
energies don't look good.
If the minimization proceeds, monitor the corresponding energies and
check the structure
after the minimization to take care that all the clashes are resolved
without introducing
odd conformations.

eddi

On Aug 8, 2008, at 3:16 AM, rebeca_at_mmb.pcb.ub.es wrote:

> Hello,
> I am trying to do a simulation of a protein+membrane using NAMD/amber.
> During the minimization, I am getting this:
>
> ETITLE: TS BOND ANGLE
> DIHED IMPRP
> ELECT VDW BOUNDARY MISC
> KINETIC
> TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG
>
> ENERGY: 0 1703673.3943 136805.9022
> 47196.3199 0.0000
> 13846442.4891 99999999.9999 0.0000 0.0000
> 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000
>
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: 1.40746e+06
> ENERGY: 1 1693389.9816 136708.8717
> 47190.9673 0.0000
> 13848767.3731 99999999.9999 0.0000 0.0000
> 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000
>
> ENERGY: 2 1683142.4203 136611.9751
> 47185.6190 0.0000
> 13851346.3909 99999999.9999 0.0000 0.0000
> 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000
>
> ENERGY: 3 1662754.8392 136418.5850
> 47174.9349 0.0000
> 13873293.1402 99999999.9999 0.0000 0.0000
> 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000
>
> (...)
>
>
> I am a bit worried about the number 99999999.9999. I have more than
> 800,000
> atoms. Could this be a problem?
>
> Thank you very much for your help.
>
> Best wishes,
>
> Rebeca García Fandiño
> Parc Cientific de Barcelona
> rebeca_at_mmb.pcb.ub.es
>
>

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================

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