[AMBER] defining a progress variable to be the z-component of some atom or group of atoms?

From: David Case <david.case.rutgers.edu>
Date: Sat, 18 Jan 2020 13:14:29 +0000

Is there a built-in way in pmemd to define a progress variable (aka
reaction coordinate) for umbrella sampling to be the z-component of the
center-of-mass of some group of atoms?

We have a lipid bilayer with the normal along the z-axis, and would like
to estimate a PMF for pulling a peptide out of the membrane.
Suggestions for other/better ways to do this are also welcome.


AMBER mailing list
Received on Sat Jan 18 2020 - 05:30:02 PST
Custom Search