Re: Minimization issue.

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Mon Aug 17 2009 - 10:33:57 CDT

your VDW energy if very high. so, apparently,
you have clashes in your system (atoms too close to each other).
if it does go like that endlessly, it seems to me that these clashes
cannot be resolved in the minimization.
btw, is there a special reason to minimize at constant pressure?
I usually do minimizations at constant volume.

eddi

On Aug 17, 2009, at 10:20 AM, Yoav Beck wrote:

> Dear all,
>
> Thanks for the help on my previous questions. I am trying to
> minimize a pope membrane (no protein yet, but lipid tails had
> already been melted) with water on top and bottom. I have done it
> previously without problem. This time when I start the minimization,
> I get this odd result :
>
> TCL: Minimizing for 2500 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 POTENTIAL TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 18740.4117 2370123.0355 44852.5867
> 202077.6674 -389262.6409 9999999999.9999
> 0.0000 0.0000 0.0000 9999999999.9999
> 0.0000 9999999999.9999 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 1403600.0000 9999999999.9999
> 9999999999.9999
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 1 nan nan nan nan nan nan nan nan nan
> GPRESSURE: 1 nan nan nan nan nan nan nan nan nan
> ENERGY: 1 19929.3605 2370494.7192 44860.0041
> 202085.4401 -389159.7118 9999999999.9999
> 0.0000 0.0000 0.0000 9999999999.9999
> 0.0000 9999999999.9999 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 1403600.0000 9999999999.9999
> 9999999999.9999
> ..
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> LINE MINIMIZER BRACKET: DX 0 0 DU 0 0 DUDX nan nan nan
> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
> and it goes on endlessly.
>
> Any help will be very appreciate.
>
> Cheers,
>
> Yoav.
>

=====================================================
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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