AMBER Archive (2006)

Subject: Re: AMBER: restraints and constant pressure

From: Myunggi Yi (
Date: Sun Sep 17 2006 - 09:23:33 CDT

Dr. Cheatham said,

To simplify the restraint code, rather than inducing a force (coordinate
deviation) every time the simulation coordinates are scaled (relative to
the restraint coordinates), it was decided to scale the restraint
coordinates as well. This effectively changes the restraint coordinates
at each step (every time the coordinates are scaled). Two problems may

(1) when you restart, and reference previous restraint coordinates (that
were not shifted), you will get an initially large restraint energy due to
the "shift", and

(2) if you are restraining multiple molecules, the relative positions of
the molecules will change as the simulation proceeds. Imagine the default
case where the density of the water is too low initially, the box has to
contract. If you are restraining two molecules, for example the two
strands of DNA, as the run continues, the restraint coordinates will shift
the molecules closer together which will force your MD coordinates to
cause the two strands to get closer. This is undesirable.

Best wishes,

MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

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