Re: Metadynamics Problems

From: Aron Broom (
Date: Mon Mar 12 2012 - 16:30:16 CDT

Just to follow-up: with more careful investigation there does not appear to
be any problem concerning (2). Also, thanks for the suggestion about the
Wall, I hadn't even realized there were separate Wall and Boundary

Thanks again,


On Thu, Mar 8, 2012 at 2:15 PM, Giacomo Fiorin <>wrote:

> Yes, that's exactly the reason why hills near or beyond the grid
> boundaries are still recorded, because not doing so would lead to ignoring
> them and generating a spurious artificial minimum right beyond the
> repulsive wall. If you set upperBoundary beyond upperWall, you have the
> annoyance that metadynamics will include the wall itself in the PMF, but at
> least you can keep the simulation always fast.
> About (2). yeah, it would be best if you can reproduce what you observed.
> Quite often if the PMF doesn't make much sense it is not because of
> configuration errors on your part, but because of the fact that the
> collective variables are not describing the system well.
> My advice is, instead of just the PMF have a closer look at the trajectory
> (both of your variable and of the entire system) to see what's going on.
> Giacomo
> On Thu, Mar 8, 2012 at 12:59 AM, Aron Broom <> wrote:
>> Hi Giacomo,
>> Thanks for the clarification about the hills, I see now that all the
>> explicit hills are indeed past the boundary of the colvars. In this
>> particular case it was a distance for a ligand to a protein, so the only
>> real "boundary" is that set in the colvar. I guess then an intelligent
>> thing to do is to increase the strength of the boundary wall constant? The
>> case where it was most obvious was a fairly unusual case where there was
>> very rapid diffusion because there was no solvent, and in most cases I
>> don't actually notice a difference, but I just wondered if something was
>> off. I see now though that if this wasn't the case, when the biasing
>> potential from the metadynamics became stronger than the parabolic wall,
>> the system would fall into an artificial minimum at the position of the
>> wall.
>> In terms of (2): what you mention is what I initially thought when I saw
>> the PMF - that setting the hill height lower had somehow caused all the
>> previous hills to be reinterpreted as having the same lower height - but
>> this isn't the case. If if I restart and only run for a short time, the
>> PMF does not change appreciably. The change only become apparent after
>> running for longer times. I haven't had the opportunity to do a thorough
>> test to see if I can understand what is happening (such as what happens
>> when the hill height is actually increased). Perhaps best if I find some
>> time for that shortly and then report back with more detailed and clear
>> information on the problem, I just thought maybe someone had seen it before.
>> Thanks for the rapid response!
>> ~Aron
>> On Wed, Mar 7, 2012 at 7:02 PM, Giacomo Fiorin <>wrote:
>>> 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
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo

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 - 23:21:45 CST