From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 08 2014 - 15:45:04 CDT
Hello Mitchell, if the "tilt" cosine function does not work for you because
of its symmetry, how about defining a "spinAngle" around an axis orthogonal
to Z? That should give you the tilt angle, but with a sign (if I
understand correctly this is what you are looking for).
On Wed, Oct 8, 2014 at 4:38 PM, Mitchell Gleed <aliigleed16_at_gmail.com>
> 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,
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:17 CST