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

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Apr 18 2016 - 06:54:37 CDT

I am using NAMD 2.11 built from source (not the pre-compiled version).

On Mon, Apr 18, 2016 at 5:10 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hello Souvik, what version of NAMD are you using? This error has been
> fixed in the latest version.
>
> Giacomo
> On Apr 18, 2016 3:37 AM, "Souvik Sinha" <souvik.sinha893_at_gmail.com> wrote:
>
>> 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
>>
>

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

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:20 CST