From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Mar 07 2012 - 17:29:38 CST
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 <akohlmey_at_gmail.com> 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 <broomsday_at_gmail.com> 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
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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