[gmx-users] Flat-bottomed potential for Sampling in particular volume

[Lukas Zimmermann]

Dear GROMACS user,

I use the pull code to pull one peptide away from a larger globular
protein. For subsequent Umbrella Sampling analyses, I want to keep the
peptide within a certain (cylindric, say) volume.
However, I want to define the longitudinal axis of the cylider running
parallel to the pull direction and
the cylinder centered in the box.

The peptide's exact pull path would run approximately near the surface of
the cylinder. Is there a way to
realize this scenario with the position_restraints  directive using
flat_bottomed function type?
As far as I understand the position_restraint directive, the volume is
always centered at the particular atom, which will be restrained. That does
not really correspond to my case.
Perhaps I'm wrong here.


Another way to put it would be having a force acting on the peptide pulling
it orthogonal
to the original pull direction back to the center longitudinal of the box
in an harmonic fashion.

I basically want to restrain the volume in the which the peptide is
sampled, but the peptide,
in its initial conformation is not supposed to be the center of this volume.


Thank you very much in advance.


Regards