Re: Net charge of the system is not zero

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jul 24 2007 - 17:00:56 CDT

It's probably a rounding error that prevents you from getting
precisely 0, but it happens to most everyone. It's nothing to worry
about though.

On Jul 23, 2007, at 8:28 AM, utiramerur_at_ecr6.ohio-state.edu wrote:

> Hi all, I am running simple simulation of DimethylEther in water
> and the net charge of the sytem in my PSF file is zero, but my log
> reports a small net charge of 5.96046e-08E. Does anyone know what
> could be the cause of this and if this small charge would affect
> the electrostatics (I am using PME).
>
> Thanks
>
> Sowmi
>
> LOG FILE
> Info: STRUCTURE SUMMARY:
> Info: 1420 ATOMS
> Info: 951 BONDS
> Info: 494 ANGLES
> Info: 21 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 1414 RIGID BONDS
> Info: 2846 DEGREES OF FREEDOM
> Info: 474 HYDROGEN GROUPS
> Info: TOTAL MASS = 8521.33 amu
> Info: TOTAL CHARGE = 5.96046e-08 e
> Info: 21 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 1414 RIGID BONDS
> Info: 2846 DEGREES OF FREEDOM
> Info: 474 HYDROGEN GROUPS
> Info: TOTAL MASS = 8521.33 amu
> Info: TOTAL CHARGE = 5.96046e-08 e
>
> >-----Original Message-----
> >From: andrea carotti [mailto:andcar_at_chimfarm.unipg.it]
> >Sent: Monday, July 23, 2007 08:46 AM
> >To: namd-l_at_ks.uiuc.edu
> >Subject: namd-l: FATAL ERROR: Bad global improper count!
> >
> >Hi all,
> >I'm getting this error and my simulation (protein) stops.
> >If then i restart the MD it goes on for a while and after some
> steps it
> >stops qith the same error. From a visual inspection everything is ok.
> >I'm running it using the last version in binary format (tcp).
> >My computing system is a cluster ibm based x3665, with mpich and sge
> >queue system (ROCKS cluster). I'm using 18 processors.
> >
> >This is the LOG with the error:
> >
> >ENERGY: 495500 391.3126 1007.2228 376.7549
> >107.2033 -353880.6957 32054.3436 0.0000
> >0.0000 62914.4988 -257029.3596 311.9644 -256981.5243
> >-257019.8884 311.7083 -116.1457 -56.7914
> >1004811.0739 0.0489 0.6264
> >
> >WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 495500
> >FATAL ERROR: Bad global improper count!
> >
> >FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> >Stack Traceback:
> > [0] _ZN10Controller9integrateEv+0x5a0 [0x821bddc]
> > [1] _ZN10Controller9algorithmEv+0x518 [0x82146d0]
> > [2] _ZN10Controller9threadRunEPS_+0xc [0x8221770]
> > [3] /home/install/namd/namd2 [0x831aa19]
> > [4] Charm++ Runtime: Converse thread (qt_args+0x72 [0x83939ca])
> >
> >Here is my configuration file:
> >;# molecular system
> >structure 1YCR_charmm.psf
> >
> ># force field
> >paratypecharmm on
> >parameters PARM.PRM
> >exclude scaled1-4
> >1-4scaling 1.0
> >
> ># approximations
> >switching on
> >switchdist 8
> >cutoff 12
> >pairlistdist 13.5
> >margin 0
> >stepspercycle 20
> >splitPatch hydrogen
> >dielectric 1
> >rigidBonds all
> >COMmotion no
> >useSettle on
> >fullElectFrequency 2
> >nonbondedFreq 1
> >
> >
> ># Periodic Boundary conditions
> >cellBasisVector1 102.493 0. 0.
> >cellBasisVector2 0. 102.493 0.
> >cellBasisVector3 0. 0. 102.493
> >cellOrigin 51.246 51.246 51.246
> >wrapWater on # wrap water to central cell
> >wrapAll on # wrap other molecules too
> >wrapNearest off # use for non-rectangular cells
> >
> >
> >#PME (for full-system periodic electrostatics)
> >PME yes
> >PMEGridSizeX 122 # Valore > vicino a quello della cella
> >PMEGridSizeY 122 #
> >PMEGridSizeZ 122 #
> >
> >#integrator
> >timestep 2.0 #unita in fs
> >
> >#output
> >outputenergies 500 #timestep per output ene
> >outputtiming 1000 #timestep per output per CPU memoria
> >e altro
> >outputpressure 1000 #timestep per output pressure (bar)
> >
> ># continuing a run
> >binaryoutput yes
> >binCoordinates 1YCR_min_equ.coor # coordinates from last run (binary)
> >binVelocities 1YCR_min_equ.vel # velocities from last run (binary)
> >extendedSystem 1YCR_min_equ.xsc # cell dimensions from last run
> >numsteps 500000 # run stops when this step is
> >reached:attiva per dyn. 1ns
> >
> >
> >
> ># molecular system
> >coordinates 1YCR_charmm.pdb
> >
> >#Output
> >outputname 1YCR_min_dyn
> >DCDfile 1YCR_min_dyn.dcd
> >DCDfreq 2000
> >restartname 1YCR_min_dyn
> >restartfreq 500
> >binaryrestart yes
> >
> >seed 12345
> >
> ># Constant Temperature Control Langevin dyn
> >langevin on # langevin dynamics
> >langevinDamping 10 # damping coefficient of 10/ps
> >langevinTemp 310 # temp (K)
> >langevinHydrogen on # Couple bath to hydrogens (on,off)
> >
> ># Constant Pressure Control
> >useGroupPressure yes # needed for rigid bonds
> >useFlexibleCell no # no for water box, yes for membrane
> >useConstantArea no # no for water box, maybe for membrane
> >
> >#Uso Langevin (volume variabile)
> >langevinPiston on #
> >langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
> >langevinPistonPeriod 200. ;# oscillation period around 100 fs
> >langevinPistonDecay 100. ;# oscillation decay time of 50 fs
> >langevinPistonTemp 310 ;# coupled to heat bath
> >
> >Thanks to all
> >Andrea
> >
> >--
> >ŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻ
> >Andrea Carotti
> >Dipartimento di Chimica e Tecnologia del Farmaco
> >Via del Liceo, 1
> >06123 Perugia, Italy
> >phone: +39 075 585 5169
> >fax: +39 075 585 5161
> >www http://rpg.unipg.it
> >personal www http://iris.chimfarm.unipg.it/users/andcar
> >
> >

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