[gmx-users] positional restraint

[Alok]

hello David,
                Yes my OD1 is protonated.Has the protonation state of 
the residue got to do something with it.
                                                                        
                                                                        
                     Thank you,
                                                                        
                                                                        
                         Alok Jain

David wrote:

>On Tue, 2004-11-30 at 01:32 +0530, Alok wrote:
>  
>
>>hello David and Xavier,
>>                         Thanks for all your responses to my previous
>>mails.I am sorry,I still have to bother you with
>>some more queries about the constraint.In the
>>process i would also like to answer few questions
>>u have asked in your responding mails.
>>
>>What is the range of differences you observe ?? Is it for the restrained
>>part or the rest of the protein ?
>>
>>The Observed distance difference is for the restrained part (the atoms
>>from the constrained residue).I have not checked the distance difference
>>between the other atoms of the protein as i expect it to vary anyway since
>>i am constraining only one residue in my protein.
>>
>>I present below data of distances (in Angstrom) between atoms of my
>>constained residue for the crystal structure as well as for the output
>>after Energy minimization using different Force constant.
>>
>>
>>                                     (Force Constant)
>>         Crystal      1000            10000              100000
>> O-OD1    2.58         3.17            2.87               2.66
>>    
>>
>Is your OD1 protonated? It should...
>
>  
>
>> O-HD21   4.86         5.27            5.13               4.95
>> O-HD22   4.75         5.35            5.06               4.83
>> H-OD1    4.73         4.76            4.75               4.75
>> N-HD21   4.62         4.57            4.74               4.71
>> N-HD22   5.58         5.62            5.65               5.62
>> H-ND2    4.94         4.66            4.80               4.87
>>
>>As we can observe even after value of 1000000,the atoms have not freezed
>>as u have mentioned in your mail.
>>
>>my corresponding ".mdp " file for EM is as follows:
>>
>>cpp                 =  /lib/cpp
>>define              =  -DFLEXIBLE
>>constraints         =  none
>>integrator          =  steep
>>nsteps              =  10000
>>;
>>;    Energy minimizing stuff
>>;
>>emtol               =  200
>>emstep              =  0.01
>>nstcgsteep          =  1000
>>
>>nstcomm             =  1
>>ns_type             =  grid
>>rlist               =  1.0
>>rcoulomb            =  2.0
>>rvdw                =  1.2
>>Tcoupl              =  no
>>Pcoupl              =  no
>>gen_vel             =  no
>>
>>If I am not able to freeze the atoms even after such high Force Constant,
>>then i am going wrong some where as you have suggested.Can you please
>>suggest the possible reason for the problem and would be thankfull if you
>>can shed some light into the possible solution.
>>
>>                                          Thank you,
>>                                           Alok Jain
>>
>>
>>
>>    
>>
>>>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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>--
>>>----------------------------------------------
>>>
>>>   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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>>>      
>>>
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