[gmx-users] positional restraint

[Xavier Periole]

David van der Spoel wrote:

>On Mon, 2004-11-29 at 15:21 +0100, Xavier Periole wrote:
>  
>
>>Alok wrote:
>>    
>>
>>>                              Though i have increased the force 
>>>constant value,I am not sure about the detrimental structural effect ( 
>>>I have read somewher that too large the force constant may result in 
>>>structural artifacts) it may have on my protein.So I would like to 
>>>know about the ideal value for the force constant such that the atoms 
>>>are constrained considerably and also that the protein does not 
>>>experience any unwanted structural deformation. 
>>>      
>>>
>>It seems that there is definitely something wrong in your restrains. A 
>>force constant of 100000 should freeze your atoms
>>    
>>
>No! Only if you take a ridiculously small time step, otherwise they will
>oscillate into oblivion.
>  
>
sorry for expressing myself a bit too fast. Oblivion seems top be much 
more adapted.

>  
>
>>at their original position. If you restrain only a part of your molecule 
>>it is reasonable to imagine that the rest of the protein
>>is responding to "existing" forces.
>>A force constant of about 500 to 1000 is ok !
>>XAvier
>>
>>
>>    
>>


-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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