From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Nov 01 2010 - 13:26:21 CDT
Dear Nishtha,
You should have also noticed the number of bad contacts decreasing as the
minimization continued. Unless your system becomes trapped in a
pathological arrangement, continuing to minimize should eventually resolve
the bad contact warnings.
Best,
Chris
On Sat, Oct 30, 2010 at 8:40 AM, nishtha mishra <nishtha_svbp_at_yahoo.co.in>wrote:
> hi,
>
> This is my log file of minimization and i am encountering this problem of
> bad contact downhill here .My minimization is running properly
> The value of vanderwaal average value is also seems weird to me.
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 3336.4541 938.4022 283.2209
> 1.0162 380581.9359 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 0.0000 683540656.5617 646716716.8984
> 111744.0000 683540656.5617 646716716.8984
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING 1492 ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 1 1.90154e+08 -7.92153e+06 2.81136e+06 -7.92153e+06 1.87147e+08
> 8.71793e+06 2.81138e+06 8.71795e+06 2.06294e+08
> GPRESSURE: 1 1.612e+08 -7.58164e+06 4.946e+06 -7.69871e+06 1.61927e+08
> 1.12054e+07 4.88932e+06 1.11196e+07 1.78859e+08
> ENERGY: 1 13268.2720 2393.8370 328.8245
> 7.9060 383377.1007 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 0.0000 194531588.3111 167328570.6596
> 111744.0000 194531588.3111 167328570.6596
>
> what could be the reason?please sort out my problem.
>
>
>
-- Chris Harrison, Ph.D. 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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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