Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Mar 25 2009 - 14:18:43 CDT

Hi David, you can let the DCD trajectory be saved more frequently to
see what's happening (DCDfreq), and play with minTinyStep and
minBabyStep to make it go faster. By default, NAMD's minimizer tryes
to stay a little on the safe side...

Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
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On Wed, Mar 25, 2009 at 1:47 PM, David Tanner <dtanner_at_ks.uiuc.edu> wrote:
> While trying to minimize a solvated structure of 70,000 atoms, the
> minimizer seems to be stuck on
>
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 3317 1.27788e+08 766912 1.61734e+06 766912 1.26235e+08
> 1.56142e+06 1.61734e+06 1.56142e+06 1.26205e+08
> GPRESSURE: 3317 1.31167e+08 1.59921e+06 1.8525e+06 15885 1.28542e+08
> 1.52692e+06 1.4571e+06 929851 1.29431e+08
> ENERGY: 3317 186524.4117 20803.2311 762.8600
> 131.4044 -89412.6070 69834715.6227 0.0000 0.0000
> 0.0000 69953524.9229 0.0000 69953524.9229
> 69953524.9229 0.0000 126742829.0978 129712883.2452
> 153900.0000 126742829.0978 129712883.2452
>
> Within 10 steps, the energy was minimized to what you see here, but
> after another 3000 steps nothing has not improved (and it won't write
> to DCD for me to view what's happening). Similar systems of mine
> minimized just fine: "MSMAWBCD" stopped being displayed well before
> 3000 steps, and other minimizations ensued.
>
> Should "MSMAWBCD" take this long or does this suggest there is
> something wrong with my structure.
>
> What would the most likely structural problems be? Could I have the
> wrong atoms bonded; my structure looked correct when I checked it?
> Could atoms be overlapping in such a way that they cannot pulled
> apart?
>
> Thank you,
> David E. Tanner
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> (217) 244 - 2905
> dtanner_at_ks.uiuc.edu
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>

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