From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 18 2016 - 06:40:09 CDT
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
>
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