Metadynamics Problems

From: Aron Broom (
Date: Wed Mar 07 2012 - 17:13:23 CST

Hello NAMD Users,

I've been using the Metadynamics module in NAMD for some time now, as it is
quite simply fantastic. I have, however, become confused by a few things
and wondered if anyone could clarify.

1) When "usegrids on" is set, my impression is that all repulsive gaussian
hills added are to be descretized onto grids, such that no individual hills
are recorded, and hence, the speed of the simulation does not slow down as
the number of hills added increases. What I've found is that a few hills
still get added periodically, and over very long simulation times (or many
many hill additions) the simulation slows down considerably, and the size
of the .colvars.state file, which holds the grids (and now also these
spurious hills) grows to mammoth proportions (hundreds of MB). Is this
supposed to happen? Has anyone else encountered this?

2) If a simulation is restarted and none of the hill parameters are
changed, everything is fine. If, however, one changes the height of hills
after a restart (still when using grids), the new spurious hills (see
above) are correctly identified as having a small height, but the effect on
the resulting PMF (and I presume the grids) is that these hills seem to
subtract from the aggregate biasing force, such that if one runs a
simulation for time t with hill height h, and then restarts with hill
height h/10 and runs for 10*t, the resulting PMF is essentially flattened
and one returns to an unbiased run (rather than simply smoothing out the
PMF as one would have hoped). Is the changing of hill heights not
something that can be done, or is it something that just can't be done
while using grids?

Again, many thanks to whomever added this feature to NAMD.


Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:44 CST