From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Mar 26 2009 - 16:51:03 CDT
It turns out that the periodic cell size was too small, and it's near
impossible to minimize overlapping triple-dense water. In any case, I've
changed MSMAWBCD so it reports the number of atoms with bad contacts and
gives up after at most 100 steps or 10 steps without progress and switches
to conjugate gradient (not that it helps in this case).
I also fixed a bug of moving fixed atoms if they had bad contacts.
-Jim
On Wed, 25 Mar 2009, David Tanner wrote:
> Giacomo,
>
> Thanks for you feedback,
>
> My DCDfreq is low enough (100) that many frames should have been
> written during the 3000 step minimization. It seems like "MSMAWBCD" is
> unwilling to write frames. I'll see if minTinyStep and minBabyStep can
> help, but I don't know if they are in effect during "MSMAWBCD".
>
> 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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>
>
> On Wed, Mar 25, 2009 at 2:18 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu> wrote:
>> 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
>> phone: (+1)-215-573-4773
>> fax: (+1)-215-573-6233
>> mobile: (+1)-267-324-7676
>> mail: giacomo.fiorin_<at>_gmail.com
>> web: http://www.cmm.upenn.edu/
>> ---- ----
>>
>>
>>
>> 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
>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:31 CST