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

From: Marimuthu Krishnan (
Date: Tue Nov 13 2012 - 13:22:57 CST


Thank you for a quick response.

I do see both colvars.state and colvars.state.old files. For most restarts,
I use colvars.state files. As you may be aware, occasionally **we end up
with incomplete colvars.state files when the computing time exceeds the
wall-clock limit. That is when I use colvars.state.old files to restart the
runs. So, there is no problem with I/O.

I will email you the output logs and the configuration file today.

There is nothing interesting happening in the standard error log.

Thanks once again.

On Tue, Nov 13, 2012 at 11:21 AM, Jérôme Hénin <>wrote:

> Krishnan,
> 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?
> Best,
> Jerome
> 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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