Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations

From: Giacomo Fiorin (
Date: Tue Nov 13 2012 - 14:11:05 CST

Hello Krishnan, if you have a massive list of hills at the ends your
boundaries may be too tight. Those hills only appear when the variables
get too close to the boundaries of the grid.

Make a new colvars configuration file with wider boundaries, and enable
rebinGrids only once (you may disable it in the later runs). This should
take care of the hills accumulated, if that is the problem.

If you still see the performance decrease, is that reproducible? That is,
have you tried to re-run the first job of the ABF or metadynamics
calculations to see if the performance is still fast?


On Tue, Nov 13, 2012 at 2:58 PM, Aron Broom <> wrote:

> I'm not sure if it is all a result of the *.colvars.state file, but it
> seems like that could be the culprit. In general what one can do is to set
> Walls for your colvars that are somewhat far (multiple hill widths) from
> the Boundary, and this will prevent the accumulation of hills in the file.
> There may be some additional options to help with this in NAMD 2.9, I can't
> recall exactly, there might be old list messages with between myself and
> Giacomo Fiorin that will have better information. But most of those
> suggestions I guess are for starting a new simulation.
> Anyway, in essence what is happening is that when your colvar gets very
> near your boundary, rather than writing the hill to the grids, the hill
> must be written directly, otherwise a significant potion of the hill would
> be ignored. Given enough time (i.e. build up of hills everywhere else) the
> metadynamics bias would push your system past the colvar boundary and it
> would become trapped there, hence the need for those hills.
> I'm not sure exactly how to solve the problem once you've already started,
> BUT, if you want to just test to make sure this IS the problem, that is
> simple. Just open your .colvars.state file, delete all the hills from the
> bottom, and try restarting your simulation. Not having the hills won't be
> a problem for restarting, and you should get a sense of how the performance
> is comparing. Sadly you'll probably also see your system become trapped
> outside the colvar boundary.
> ~Aron
> On Tue, Nov 13, 2012 at 2:47 PM, Marimuthu Krishnan <
>> wrote:
> > Aron,
> >
> > I do not use NAMD benchmarking to evaluate the performance. I simply use
> > the trajectory length obtained in 24 hours as a measure of performance.
> >
> > The *.colvars.state files are > 10 MB and in some cases it is even
> greater
> > than 20 MB. The "usegrids" option is ON by default. I use default values
> > for 'hillwidth' and 'hillweight'. Although one could vary 'hillwidth' and
> > 'hillweight' to achieve better performance/accuracy, it is not clear to
> me
> > why restart runs perform poor than new runs for same values of
> 'hillwidth'
> > and 'hillweight'. Do you have some suggestions for me to improve the
> > performance of restart runs at this point?
> >
> > You are correct. I see a massive list of hills at the bottom of the
> > *.colvars.state file.
> >
> > By the way, I am not sure whether to keep 'rebinGrids' ON or OFF for
> > restart runs. I have kept it 'OFF' (default value). Does it play any role
> > in the performance?
> >
> > best,
> > Krishnan
> >
> >
> > On Tue, Nov 13, 2012 at 11:47 AM, Aron Broom <>
> wrote:
> >
> >> One possibility is that the performance decrease is actually continuous.
> >> You should have a *.colvars.state file, how large is it?
> >>
> >> If you're saying the performance decreases because of the NAMD
> >> benchmarking that happens at the beginning of the run, this won't be
> >> accurate in the case where your *.colvars.state file becomes very large
> >> (i.e. > 10MB) during the course of the simulation. What you'll see in
> that
> >> case is a gradual decrease in performance over time, so make sure your
> >> performance numbers are based on timings taken throughout the simulation

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