[gmx-users] Bias potential during umbrella sampling

Meena Singh meenadcat at gmail.com
Fri May 11 11:33:24 CEST 2018

Dear GROMACS users,

Currently I am doing umbrella sampling for adsorption of molecule on solid
surface. I have frozen the coordinates for solid surface and pulling the
molecule towards the surface.

I would like to know that while using options pull-geometry = distance and
pull-dim = N N Y is same as the options pull-geometry = direction and
pull-vec = 0 0 1?

I am confused regarding the bias potential applied on the molecule, whether
it is applied in all x, y, z coordinate of molecule or only in z coordinate
of molecule for the above two scenarios?

Thanking in advance for the help.


Meena Singh

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