Re: checkpoint software for NAMD?

From: Gianluca Interlandi (
Date: Thu Sep 21 2006 - 16:55:46 CDT

What I usally do in these cases is I put the restart frequency equal or
more often than the DCD save frequency. Before restarting you need to
update "firsttimestep" in your config file because unfortunately the
restart files don't store at what step they were saved so that NAMD could
automatically read it. But if you use "restartsave on" it will append the
timestep to the file name. So you can implement a script which figures out
from the name of the restart files what the last step was and use "sed" to
update "firsttimestep" in your config file. You also need to update
"binvelocities", "bincoordinates" and "extendedSystem" to point to the
latest restartfiles.

The alternative is to use "restartsave off" but then your script has to
figure out the last step from the NAMD log file and round it down to the
step at which the last restart files have been written. The advantage is
that you don't need to update "binvelocities", "bincoordinates" and

It's not as complicated as it sounds like, just a matter of putting some
UNIX commands into a batch script.

I hope it helped a bit,


On Thu, 21 Sep 2006, Dan Strahs wrote:

> Hi:
> I'm running NAMD on some i386 machines using an FC4 Linux. I will need to
> reboot the machines periodically into another OS, unfortunately interrupting
> the NAMD jobs.
> I would like to checkpoint the NAMD jobs to restart at the EXACT step in the
> cycle at which they were interrupted. Restart files could work, but I would
> have to conservatively estimate the restart frequency.
> Is there a checkpoint capacity built into NAMD? Does anyone have any
> experience with checkpoint software for Linux environments?
> Dan Strahs

Dr. Gianluca Interlandi
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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