The Amber11 manual, in Section 4.5.2, p.108 gives an example of SMD by changing the distance between two atoms. Given that the position of the two atoms are defined by Cartesian coordinates, the push or pull between the two atoms would be directional.
My understanding is (was) that SMD applies spherical restraints and therefore does not specify a certain direction.
Any clarification on the directionality or non-directionality of the SMD method would be greatly appreciated.
Regards
George
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Received on Thu Dec 13 2012 - 04:00:02 PST
