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.
Josh
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
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