[gmx-users] RMS deviation after position restraint dynamics

[Mark Abraham]

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?

You should read in the manual about how position restraints are implemented.

If you wanted zero RMS deviation in one of your observables, perhaps you 
should re-think why you are running *dynamics*. :-)

Mark