From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
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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