Re: colvars PMF history problem

From: Axel Kohlmeyer (
Date: Mon Mar 07 2011 - 09:27:19 CST

2011/3/7 Ajasja Ljubetič <>:
> Dear NAMD users,
> As a quick hack I wanted to see how the PMF changes during the simulation.
> So  at the end of the conf file I ran:
>   for  {set i 1} {$i<=$hsteps} {incr i 1} {
>     run $numsteps
>     set snum [format "%04d" $i]
>     print "Saving  pmf to $outputname.$snum.pmf"
>     file copy -force $outputname.pmf  $outputname.$snum.pmf
>   }
> basically I run the simulation in parts and copy the pmf every $hsteps.
> The problem is that after the first run the log file is field with:
> colvars: Overwriting colvar trajectory file "out/run/chi1.colvars.traj".
> ERROR: Error on renaming file out/run/chi1.colvars.traj to
> out/run/chi1.colvars.traj.BAK: Permission denied
> The lines gets added every time the colvar.traj is updated, but otherwise
> the simulation proceeds OK.
> If I change  colvarsTrajAppend to on the error changes to:
> colvars: Appending to colvar trajectory file "out/run/chi1.colvars.traj"
> If I set the colvarsTrajFrequency to 0 then the problem disappears (but I'm
> left without a traj file).
> Is this a know problem? I'm running NAMD 2.7 on win32.

i would suspect that it is a problem related to windows
and the fact that it has different file system semantics
than other operating systems. e.g. on unix/linux systems
you can delete/rename/overwrite a file while it is still held
open by some other process. the old file will become "invisible",
but available until the last process that holds the file descriptor
terminates, at which point also the storage is released.
everything else will just see the new file (or no file). on
windows these things are different. i would not expect a
windows version of a simulation software that is mostly
used on unix-like machines to be as thoroughly tested.


> Best regards,
> Ajasja Ljubetič,
> Young reasercher,
> Laboratory of biophysics,
> Institute Jožef Štefan,
> Ljubljana, Slovenia

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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