Re: Minimization issue.

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Aug 18 2009 - 10:51:20 CDT

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                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Mon, Aug 17, 2009 at 10:43 AM, Chris Harrison <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                            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>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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