[gmx-users] Umbrella Sampling with Direction-Periodic Pulling

[Daniel Kozuch]

Hello,

I am using a pull code with geometry=direction-periodic and attempting to
use gmx wham to construct the free energy. I believe 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. Or is the best option to simply edit the pullx
files?

Thanks,
Dan