From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jun 13 2013 - 04:45:19 CDT
I've just implemented a maxForce option for ABF, that should let you avoid the peaks in biasing force near the wall.
You can get the code there: http://colvars.github.io
----- Original Message -----
> Hi Zachary,
> This problem can be annoying, it is caused when the discretization of
> the mean force used by ABF breaks down due to a singularity in the
> PMF. You can take two kinds of measures to limit this:
> 1) avoid biasing the wall region: maybe not by restraining the
> coordinate, but rather by changing the grid limit
> (lower/upperBoundary) so that the very steep region gets off-grid.
> 2) refine the grid. If you have several windows, this could be done
> locally, close to the hard wall.
> 3) one option I've been pondering is to add a cap on the biasing
> force applied, which could work in your case. That could be
> implemented soon, in which case we'll let you know about it.
> ----- Original Message -----
> > I'm doing simple adsorption energy calculations using ABF onto a
> > hard
> > surface (one coordinate). Everything works fine, but often the
> > simulation gets stuck trying to resolve the potential very near the
> > surface, which is very large but not interesting or important.
> > I've tried restraining the colvar to a minimum of several angstroms
> > from the surface which helps, but the offset is different for each
> > molecule (different adsorption distances), and if it's too large
> > the
> > minimum in the resulting PMF is missed.
> > Does anyone have a good suggestion for doing ABF calculations when
> > there is a hard wall present?
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:18 CST