[gmx-users] Re: COM translation

[David van der Spoel]

Janne Hirvi wrote:

>Hello David!
>
>I don't understand how could I use simulated annealing protocol. Yes, I am
>interested only in the final structure, but still I have no clue what do you
>mean. My problem is that I get COM translation about 20-25nm/ns without COM
>motion removal and I was interested how much this effects on my simulation
>temperature. If I am right, the influence is not so "significant". At least the
>system is not frozen and still have vibrations and other high frequency motions
>as it really should have at high temperature (450-600K). 
>
>Janne
>  
>
Just repeated heating and cooling will make the convergence a lot faster.
Check mdp options.


>  
>
>>Janne Hirvi wrote:
>>
>>    
>>
>>>Hello!
>>>
>>>I am trying to produce structured (stripes etc.) polymer surfaces by
>>>      
>>>
>>pressing
>>    
>>
>>>bulk polymer step by step between two grid surfaces. One grid surface is
>>>      
>>>
>>planar
>>    
>>
>>>and the other one is negative from the wanted surface structure.
>>>
>>>I have problem with large COM translation in the direction of stripes, but
>>>however I think that I can't use linear -option for center of mass motion
>>>removal because the shape of the systems should/will change during
>>>      
>>>
>>simulation
>>>from enterily planar to some modified shape.  
>>    
>>
>>>So do I get misinterpret simulation temperatures without COM motion removal
>>>      
>>>
>>and
>>    
>>
>>>what could I possibly do to solve this problem? At least there is still
>>>vibrational and torsional motions too, but can I somehow see what is the
>>>      
>>>
>>real
>>    
>>
>>>temperature without COM translation? I think that g_energy ang g_traj give
>>>temperature based on "total velocities"? 
>>> 
>>>
>>>      
>>>
>>Are you interested in the final structure only? In that case you could 
>>try some kine of simulated annealing protocol.
>>
>>
>>    
>>
>>>Thanks for any help or comments! 
>>>
>>>
>>>Janne
>>>
>>>      
>>>
>>------------------------------------------------------------------------------
>>    
>>
>>>Janne Hirvi, MSc(Physical Chemistry), Researcher
>>>University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
>>>      
>>>
>>FI
>>    
>>
>>>Tel: +358 13 2514544 & +358 50 3474223
>>>E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
>>>      
>>>
>>------------------------------------------------------------------------------
>>    
>>
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>>>
>>>      
>>>
>>-- 
>>David.
>>________________________________________________________________________
>>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>>Dept. of Cell and Molecular Biology, Uppsala University.
>>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>>phone:	46 18 471 4205		fax: 46 18 511 755
>>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>    
>>
>
>
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>  
>


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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