From: Riley Workman (workmanr_at_duq.edu)
Date: Thu May 08 2014 - 12:08:13 CDT
I am trying to generate a PMF using ABF and am having trouble getting the PMF to plateau. I have hideJacobian set on.
I use the selectConstraints x and y commands to restrict two water molecules to the z-coordinate. I am trying to generate a dimerization of the two water molecules from a specific conformation, thus the constraints. I am performing the ABF on a distance colvar between the oxygens of the two waters.
When I run such a simulation without the constraints, I get a lovely smooth water-water PMF that plateaus at around 3.5 kcal/mol. Keep in mind I am setting hideJacobian to on, so the PMF should plateau. I have read the NAMD information on ABF and am aware that constraints on atoms involved in the distance coordinate can disrupt the accuracy of the PMF. My thought was that since the x and y constraints are orthogonal to the distance colvar, that might not happen.
Can anyone with expertise in ABF lend any insight on why this happens and how I might circumvent the problem? I realize that I could use umbrella sampling or some other method of measuring the PMF, but I have performed some other related calculations with ABF and would like to use it with this one as well, if possible.
Thanks for any and all suggestions.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:23 CST