[gmx-developers] Brainstorming ideas for minimally painless incorporation of an MC barostat (later MC moves in general)

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Jul 17 18:10:39 CEST 2014

>Is there any reason not to use molecular (center of mass) scaling to
>avoid meddling with constraints?

Either molecular COM scaling or constraint system COM scaling seem like a
good idea to me.

Constraint system scaling might be more appropriate in the case of things
like entire proteins; you probably don't want all of the waters to scale
their locations, and not the protein, because that would lead to high
rejection probability as the waters move WRT the protein center of mass
but not the individual protein atoms far from the COM.

One thing I'm trying to think through; in the calculation of the virial,
even though though the holonomic constraint lengths will not have changed,
the external forces on those atoms will have changed when the atoms are
moved.  I may be overthinking this though, and perhaps this effect is
unimportant; the velocities parallel to the bonds will still be zero.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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