[gmx-users] energy minimization

[Itamar Kass]

  Shalom Flavia

If I got you right, the problem are arose when you do EM. If so, why not 
to minimize the water embedded protein. do a small MD run to see that 
everything is O.K. Latter add the TFE and minimize the system, you can 
add the TFE molecules in part – not all the molecules at the same time. 
Do not forget to do EM and few ps of MD between steps.



flavia at lncc.br wrote:

>Thanks for answering, Itamar.
>
>But what I have, in fact, is the same error as Hector,
>
>Fatal error: ci = -2147483648 should be in 0 .. 2743
>
>When I use double precision I can ocasionally overcome this problem.  But I
>still have large variations in energy and I have problems when I proceed with
>molecular dinamics.
>
>I know it happens because of the inclusion of TFE molecules.  I was advised to
>make a separete program, out of gromacs, for the inclusion of TFE.  But before,
>I would like to certify myself if I couldn't solve this problem with GROMACS.
>
>Flavia
>
>Citando Itamar Kass <ikass at cc.huji.ac.il>:
>
>  
>
>>   This indicats thet your system was minimized, as long as you saw lowering
>>of
>>the energy during the EM.
>>      Itamar.
>>
>>
>>Quoting flavia at lncc.br:
>>
>>    
>>
>>>Hi everybody,
>>>
>>>I'm a new gromacs user and I am having problems while trying to minimize
>>>energy.
>>> I have a system with Protein + TFE + water and only get the same kind of
>>>result:
>>>
>>>Steepest Descents converged to machine precision in 113 steps,
>>>but did not reach the requested Fmax < 100.
>>>Potential Energy  = -1.59634647278947e+13
>>>Maximum force     =  1.11162275955399e+25 on atom 469
>>>Norm of force     =  1.57207198280386e+25
>>>
>>>I'd like to know how can I improve results, once I can only realize a
>>>molecular
>>>dynamics after the system is reasonably stable.
>>>
>>>I'd appreciate any help.
>>>
>>>Thanks,
>>>
>>>Flavia
>>>
>>>
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>>>      
>>>
>>
>>
>>********************************************
>>Computers are like airconditioners... They don't work well with Windows
>>open.
>>********************************************
>>
>>===========================================
>>| Itamar Kass
>>| The Alexander Silberman
>>| Institute of Life Sciences
>>| Department of Biological Chemistry
>>| The Hebrew University, Givat-Ram
>>| Jerusalem, 91904, Israel
>>| Tel: +972-(0)2-6585146
>>| Fax: +972-(0)2-6584329
>>| Email: ikass at cc.huji.ac.il
>>| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
>>============================================
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>
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>
>
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