[gmx-users] positional restraint

Xavier Periole x.periole at chem.rug.nl
Mon Nov 29 15:21:39 CET 2004

Alok wrote:

> hello Xavier,
>                    thank you for your reply.I checked my ".tpr file" 
> using gmxdump.The number reported in the output for POSRES is not the 
> number of atoms restrained.Also I checked that the atoms restrained 
> are the ones from my residue.So i am now clear that the required atoms 
> from my residue are selected for restrain. 

So you are saying that the output does not give the right number of 
restrains that it is actually creating !!
That should be investigated !! Next version !!

>            I have a small query to make about the value of force 
> constant.I tried using 1000.I then checked the distances between the 
> constrained atoms after energy minimization and found considerable 
> change in the distances between the atoms.I then increased it to 
> 1000000,the distance difference has reduced but still the distance 
> between some atoms has changed quite a bit. 

What is the range of differences you observe ?? Is it for the restrained 
part or the rest of the protein ?

>                             I also tried to constrain my whole protein 
> and changed the force contant values from 1000 to 1000000 and cheked 
> the animation (using ngmx),I still  find considerable movement for my 
> protein. 

Also the restrained part ?

>                               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
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 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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