[AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate

From: Dail Chapman <DChapman8112.ScrippsCollege.edu>
Date: Sun, 07 Oct 2012 16:57:08 -0700

Dear All,
 I am an undergraduate researcher at Scripps College in California, and am trying to partition various small molecules through a lipid bilayer membrane in Amber12. It seems most logical to use umbrella sampling with the z-axis (i.e., the axis perpendicular to the plane of the membrane) distance between the membrane c.o.m. and small molecule c.o.m. as the reaction coordinate. Is there a tutorial program available for this, as I have not used said technique before? Or would anyone have a suggestion for an alternative technique? Any help would be much appreciated. Thank you for your time, -Dail

AMBER mailing list
Received on Sun Oct 07 2012 - 17:00:03 PDT
Custom Search