[gmx-users] Umbrella Sampling with Direction-Periodic

Daniel Kozuch dkozuch at princeton.edu
Tue Aug 1 22:14:42 CEST 2017


I am using a pull code with geometry=direction-periodic and attempting to
use gmx wham to construct the free energy. The pulling code is doing what I
would like it to, but as might be expected from direction-periodic, when
the pull distance is more than half the box length the distance is written
as negative.

Is there some way to have the pull files written with positive (greater
than half the box length) distance so that gmx wham will work properly? For
example, if the box is 10 nm long, I would like the pull distance to be
written as 7 nm, not -3 nm.

I have tried editing the pullx.xvg files, but as the .tpr files must still
include the original shortest periodic distance, this does not correct the


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