Umbrella sampling tilt with respect to Z-axis

From: Mitchell Gleed (
Date: Wed Oct 08 2014 - 15:38:29 CDT

I am working on a procedure for 2D umbrella sampling of a ligand through a
membrane protein. The two dimensions I hope to explore are Z-distance
(using distanceZ from the colvars module) and tilt angle (hopefully using
tilt from the colvars module) of the ligand to generate a 2-D PMF.

I might not fully understand, but in my testing, and as explained in the
User Guide, the cosine of the tilt angle is measured between the atoms of
interest and reference atoms with 1 being parallel and -1 being
antiparallel to the reference atoms. However, the protein is asymmetric,
and a reported deviation in 10 degrees of the ligand, for example, doesn't
tell me whether it tilted toward +Z or -Z space, where I would expect the
ligand to behave differently. Furthermore, I'm not sure I could use tilt
with 2D-US-REMD as I've planned (based on the
NAMD_Source_2.10b1/replica/umbrella2d example), since replica bias centers
would not distinguish between +Z/-Z tilt change.

I'm considering post-processing the trajectories and measuring cos(theta)
with respect to the Z axis and then using this data to generate the PMF,
but disk space becomes a big issue, and it wouldn't solve the
replica-exchange limitation. (At which point I could switch to 1D REMD for
distance and employ constant tilt constraints.)

Can the tilt colvar be adjusted to measure the cosine of the tilt angle
with respect to an axis, rather than with respect to reference coordinates
(such as Z)? Or is there another path I could take or colvar to use to
study this dimension?

Thank you,


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