[gmx-users] RMS deviation after position restraint dynamics

Joshua Adelman jadelman at berkeley.edu
Mon May 18 08:56:30 CEST 2009

A restraint is not a constraint, and assuming that you are simulating  
your system at a finite temperature, you should expect to see some  
fluctuations in a given atom's position.


On May 17, 2009, at 11:47 PM, sukesh chandra gain wrote:

> Dear All,
> I am running position restraint dynamics to restrain the atom  
> positions of the protein to restrict their movement in the  
> simulation. Then, how could there be any RMS deviation for the  
> protein before and after the position restraint dynamics run?  
> (Although the deviation is very little).
> Could you please explain why is the deviation?
> Thank You,
> Regards,
> Sukesh
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Joshua L. Adelman
Biophysics Graduate Group              Lab: 510.643.2159
218 Wellman Hall                                Fax: 510.642.7428
University of California, Berkeley     http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA                   jadelman at berkeley.edu

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