ERROR: ofstream_namd::close() called when file is not open

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Apr 18 2016 - 02:36:33 CDT

Hi,
I am getting this error during my simulation.

colvars: Writing the state file "step5_production.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step5_production.colvars.traj".
colvars: Writing the state file "step5_production.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step5_production.colvars.traj".
WRITING COORDINATES TO DCD FILE step5_production.dcd AT STEP 2578000
colvars: Writing the state file "step5_production.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step5_production.colvars.traj".
colvars: ABFHISTORYFILE 2580000
colvars: Writing the state file "step5_production.restart.colvars.state".
colvars: Synchronizing (emptying the buffer of) trajectory file
"step5_production.colvars.traj".
colvars: Saving collective variables state to
"step5_production.colvars.state".
FATAL ERROR: ofstream_namd::close() called when file is not open

Programme is running well throughout the simulation but only at the last
output writing, this error statement is occurring.

My configuration file :

structure ../step3_pbcsetup.xplor.ext.psf
coordinates ../step3_pbcsetup.pdb

set temp 303.15;
outputName step5_production;

set inputname step4_equilibration;
binCoordinates $inputname.coor;
binVelocities $inputname.vel;
extendedSystem $inputname.xsc;

restartfreq 10000;
dcdfreq 2000;
dcdUnitCell yes;

xstFreq 10000;
outputEnergies 10000;
outputTiming 10000;

# Force-Field Parameters
paraTypeCharmm on;
parameters toppar/par_all36_prot.prm
parameters toppar/toppar_water_ions.str

# These are specified by CHARMM
exclude scaled1-4

# Integrator Parameters
timestep 2.0; # fs/step
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

# PME (for full-system periodic electrostatics)
source checkfft.str

PME yes;
PMEInterpOrder 6; # interpolation order (spline order
6 in charmm)
PMEGridSizeX $fftx; # should be close to the cell size
PMEGridSizeY $ffty; # corresponds to the charmm input
fftx/y/z
PMEGridSizeZ $fftz;

# Constant Pressure Control (variable volume)
useGroupPressure yes;
useFlexibleCell no; # yes for anisotropic system like
membrane
useConstantRatio no; # keeps the ratio of the unit cell in
the x-y plane constant A=B

langevinPiston on; # Nose-Hoover Langevin piston
pressure control
langevinPistonTarget 1.01325; # target pressure in bar 1atm = 1.01325bar
langevinPistonPeriod 50.0; # oscillation period in fs. correspond to
pgamma T=50fs=0.05ps
                                              # f=1/T=20.0(pgamma)
langevinPistonDecay 25.0; # oscillation decay time. smaller value
correspons to larger random
                                       # forces and increased coupling to
the Langevin temp bath.
                                       # Equal or smaller than piston period
langevinPistonTemp $temp; # coupled to heat bath

# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps (keep
low)
langevinTemp $temp; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens

##################################################
## ABF parameters ##############
##################################################

colvars on
colvarsConfig abf-2-bb.in

##############################################

# run
firsttimestep 80000;
run 2500000; # 5ns

Collective variable output frequencies:

colvarsTrajFrequency 1000
colvarsRestartFrequency 1000

"step5_production.colvars.traj" & "step5_production.colvars.state" files
are actually written up to 2580000 steps (which is exactly the last step of
the run) while step5_production.restart.xsc is written up to 2570000. I
can't understand what does it mean.Please help me out of it.
Thank you. 

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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