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

From: Jérôme Hénin (
Date: Tue Nov 13 2012 - 10:21:19 CST


Thank you for this report.

In principle the restart file has the extension colvars.state. The .old
extension denotes a backup file, if you only see that, it might indicate
some sort of I/O issue.

Can you send me (off-list) a colvars input file, and a series of NAMD
standard output logs that shows the performance decrease? I would at least
need that to try and diagnose the problem.

Finally, can you check the standard error log and see if there is anything
of interest in there?


On 13 November 2012 15:42, Marimuthu Krishnan <> wrote:

> Hello everybody,
> While calculating free energies using the Collective Variable Module
> implemented in NAMD 2.9, I noticed something unusual. Both ABF and
> metadynamics calculations run perfectly fine when I perform new
> calculations. When I try to restart my simulations (both for ABF and
> metadynamics), I notice 4-5 fold decrease in performance (relative to a new
> run) irrespective of the type of reaction coordinate (distance-based or
> angle-based) used. These calculations were run on Kraken (NICS) and same
> number of cores was used for both the fresh and restart runs. I do remember
> that I did not have this problem before when using earlier versions of
> NAMD. I would appreciate help from experts.
> A related minor issue with naming of the restart file. One of the output
> files from ABF/metadynamics is named file_rst.colvars.state.old but if you
> want to restart a run using this old restart file, NAMD 2.9 expects its
> name be file_rst.old.colvars.state. It would be useful if this mismatch in
> names is fixed.
> Thanks
> Krishnan

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