Re: Metadynamics Problems

From: Axel Kohlmeyer (
Date: Wed Mar 07 2012 - 17:22:46 CST


two items:

1) you forgot one *very* important piece of information:
    what version of NAMD exactly are you using?

2) the documentation gives clear credit to the authors
   of the module (giacomo fiorin and jerome henin).

to add to the praise. i am currently interfacing the
colvars code to another MD code, and it has been
a breeze with only very minor issues to work out.


On Wed, Mar 7, 2012 at 6:13 PM, Aron Broom <> wrote:
> 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
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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