Distance XY-colvars

From: Alex Liu (liu.alex77_at_yahoo.com)
Date: Tue Jan 04 2011 - 15:56:56 CST

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). If what I said
above is right, then I can conclude that the program moves rc between 0 and 0.5
and ignores negative values. Is this right?


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