colvars PMF history problem

From: Ajasja Ljubetič (
Date: Mon Mar 07 2011 - 08:43:08 CST

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.

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

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