From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Wed Jan 05 2011 - 16:12:32 CST
Hi Alex, you're right on both points, the definition is the same as the
formula you wrote (rc) and its values are always greater than or equal to
zero. You can guess by yourself that setting a negative lowerBoundary does
not make a lot of sense, although it's harmless.
If you choose to put a harmonic wall on the upper boundary, please allow for
some tolerance above there. If 1.3 Å is too high for you, increase
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
On Tue, Jan 4, 2011 at 4:56 PM, Alex Liu <liu.alex77_at_yahoo.com> wrote:
> Dear NAMD users,
> In order to confine the ion movement in XY plnae in clovar, I am using
> "distanceXY" variable and I have a couple of questions about it.
> How the distance (the range between lower boundary and upper boundary) is
> defined in this case? Is it the same as: rc=(rx^2+ry^2)^1/2 ? If so, I
> assume that both lower boundary and upper boundary should be equal or
> greater than zero. Is this true?
> I ran a test with lower boundary=-0.5 and upper boundary=0.5 and in
> distance xy reported by the program (.traj file), it just changes this value
> between 0 and 1.3 (which 1.3 is probably because the force is not enough)--0015175cdeec4d9cda049920b04b--
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