[gmx-users] Bias potential during umbrella sampling

[Viveca Lindahl]

Hi Meena,

No, they are not generally the same. The reaction coordinate using
'distance' is the norm of the COM distance vector (>=0). Using direction,
it's the projection onto the given vector (possibly negative).


--
Viveca


On Fri, May 11, 2018 at 11:33 AM, Meena Singh <meenadcat at gmail.com> wrote:

> 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.
>
> Regards
>
> Meena Singh
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