From: utiramerur_at_ecr6.ohio-state.edu
Date: Mon Jul 23 2007 - 08:28:25 CDT
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
>
>--
>¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
>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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