[gmx-users] PMF calculation using pull code (constraint force method): constrained atom seems to be moving

Nickle Fan nicklefan at gmail.com
Fri Apr 3 03:14:49 CEST 2009

Dear gmx-users:

I am performing a PMF calculation using the pull code. I selected one fixed
atom as a reference group and constrained another atom with respect to this
reference group so that their separation in the x- and z-directions remain
constant. After running the simulation, I visualized the trajectory and
found that the constrained atom dances around the expected position (it did
not drift away though).

Is this expected at all? I had thought that when I constrained the atom with
respect to the reference group, its position should remain precisely as
defined by the constraints.

I am using the NVT ensemble.


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