From: Yoav Beck (ucbpybe_at_ucl.ac.uk)
Date: Wed Aug 19 2009 - 07:11:21 CDT
Dear Chris, Eduard, and all namd's users,
Thanks for your help. You were both right, after inspection of the pdb
files, I realize there were clashes all over the place. It happened when
I minimized the headgroups (leaving everything else fixed).
While I am at it, do you know why, some simulations get stucked. I mean
they reach a certain step and then stay there forever, the processors
still working. When I restart from the same step or slightly earlier,
then it goes past than point for a few hundreds steps and then get
stucked again. Before getting stuck everything seems going well. It
happen both during minimization or equilibration.
Thanks.
Cheers,
Yoav.
Chris Harrison wrote:
> Yoaz,
>
> Something else that occurred to me: check if your cutoff and
> switchdist values are the same ... if so, they shouldn't be, make
> switchdist ~1-2 Ang lower than cutoff.
>
> Chris
>
>
> --
> 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 <mailto:char_at_ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
> On Mon, Aug 17, 2009 at 10:43 AM, Chris Harrison <charris5_at_gmail.com
> <mailto:charris5_at_gmail.com>> wrote:
>
> Yoaz,
>
> As Eddi said, this is indicative of high nuclear clashes. A
> suggestion --> check to see if any atoms are overlapping
> (literally: have the same coordinates) in the initial pdb. For
> various reasons involving topology definitions and pdb names, this
> can occur and often one finds these overlapped atoms at
> coordinates: 0.0, 0.0, 0.0, so this may be something for which to
> specifically watch.
>
>
> Chris
>
>
> --
> 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 <mailto:char_at_ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
>
> On Mon, Aug 17, 2009 at 10:33 AM, Schreiner Eduard
> <eschrein_at_ks.uiuc.edu <mailto:eschrein_at_ks.uiuc.edu>> wrote:
>
> 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/
> <http://www.ks.uiuc.edu/%7Eeschrein/>
> =============================================
>
>
>
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