Re: Metadynamics Problems

From: Giacomo Fiorin (
Date: Wed Mar 07 2012 - 18:02:59 CST

Hello Aron, and thank you for the compliments :-)

(1) is a fully normal behavior. The issue is that whenever you go beyond
the boundaries of the grid, the biasing forces suddenly disappear. For
this reason, as a safety precaution the metadynamics bias stores all those
gaussians that are near the boundary, so that they can be still used when
you're off the grid. In your case, it looks like you keep reaching the
boundaries of the grid very very often.

Also, the fact that your simulation slows down (and not just the startup
phase when the file is read) suggests that you not only get close to the
boundaries, but you are going outside of them as well. At that point, the
advantage of the grids disappears.

You should expand the boundaries to the full range of values of your
variable(s), plus a buffer the size of a Gaussian.

If you're in the situation where values close to the boundary are visited
often but the variable never goes beyond it (e.g. a RMSD variable around
zero), you can safely delete those gaussians from the state file, because
they're never going to be used.

But as I said, if the step performance is slow, it seems that you are
indeed using those gaussians and therefore should expand the grid to get
rid of them.

In (2) you seem do be doing something like well-tempered metadynamics, that
will be available soon.

But I don't understand the results you got: are you saying that after
restarting while setting smaller hills, the smaller height affects not only
the new hills, but also the existing PMF up to that point?

On Wed, Mar 7, 2012 at 6:29 PM, Aron Broom <> wrote:

> Thanks Axel,
> I'm using NAMD 2.8 (2011-05-31), the latest non-nightly build release.
> Oh I see, they contributed the entire colvars module, how wonderful,
> thanks a lot to them!
> ~Aron
> On Wed, Mar 7, 2012 at 6:22 PM, Axel Kohlmeyer <> wrote:
>> aron,
>> 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.
>> cheers,
>> axel.
>> 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.
> --
> 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