CHARMM Element doc/pbeq.doc 1.1#File: PBEQ, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Poisson-Bolztmann Equation Module The PBEQ module allows the setting up and the numerical solution ofthe Poisson-Boltzmann equation on a discretized grid for a solute molecule.Attention: Problems should be reported to . Benoit Roux at [email protected], phone (212) 746-6018 . Wonpil Im at [email protected] . Dmitrii Beglov at [email protected]* Menu:* Syntax:: Syntax of the PBEQ commands* Function:: Purpose of each of the commands* Examples:: Usage examples of the PBEQ module#File: PBEQ, Node: Syntax, Up: Top, Previous: Top, Next: Function Syntax[SYNTAX PBEQ functions]Syntax:PBEQ enter the PBEQ moduleEND exit the PBEQ moduleSubcommands:SOLVe PB-theory-specifications solver-specifications grid-specifications iteration-specifications charge interpolation-spec. boundary potential-spec. dielectric boundary-spec. physical variable-spec. membrane-specifications spherical droplet-spec. orthorhombic box-spec. cylinder-specifications solvation force-spec. atoms-selectionITERate PB-theory-specifications solver-specifications iteration-specifications ENPB [INTE atoms-selection] CAPAcitance COUNTERIONWRITE property [[CARD] [write-range]] [UNIT integer]READ [PHI] [PHIX] [FKAP] [MIJ] [UNIT integer]COOR coordinate-manipulation-commandSCALar scalar-manipulation-commandHELPRESETPB-theory-specifications::= [NONLinear] [PARTlinear] default : linear PB by default (no need to specify)NONLin [.FALSE.] : non-linear PBEQ solverPARTlin [.FALSE.] : partially linearized PBEQ solversolver-specifications::=[OLDPB] [OSOR] [UNDER] [[FMGR] [NCYC integer] [NPRE integer] [NPOS integer]]default : SOR (Successive OverRelaxation) method for linearized PBOLDPB [.FALSE.] : old PBEQ solver (used in c26a2)OSOR [.FALSE.] : optimization of the over-relaxation parameterUNDER [.FALSE.] : Under-relaxation for non-linear and partially linearized PBEQ solvers with fixed LAMBda valueFMGR [.FALSE.] : full multigrid methodNCYC [100] : maximum number of cycles (in FMGR)NPRE [2] : number of relaxation for PRE-smoothing (in FMGR)NPOS [2] : number of relaxation for POST-smoothing (in FMGR)grid-specifications::= [NCEL integer] [DCEL real] [NCLX integer] [NCLY integer] [NCLZ integer] [XBCEN real] [YBCEN real] [ZBCEN real]NCEL [65] : number of grid point in 1D for a cubicDCEL [0.1] : size of grid unit cellNCLX [NCEL] : number of grid point in X for general parallelepipedNCLY [NCEL] : number of grid point in Y for general parallelepipedNCLZ [NCEL] : number of grid point in Z for general parallelepipedXBCEN [0.0] : the center of a box in XYBCEN [0.0] : the center of a box in YZBCEN [0.0] : the center of a box in Ziteration-specifications::=[MAXIter integer] [DEPS real] [DOMEga real] [LAMBda real] [KEEPphi]MAXIter [2000] : number of iterationsDEPS [0.000002] : parameter (tolerance) of convergence DOMEga [1.0] : initial mixing factorLAMBda [1.0] : initial mixing factor (LAMBda = DOMEga)KEEPphi [.FALSE.] : Use the potential from previous calculation as a initial guess for current calculationcharge interpolation-spec.::= [BSPLine]default : the trilinear interpolation methodBSPLine [.FALSE.] : the Cardinal B-spline method is used?boundary potential-specifications::= [ZERO] [INTBP] [FOCUS] [PBC] [NPBC] [NIMGB integer] default : use the Debye-Huckel approximation at each boundary point use XY periodic boundary conditions in membrane calculation INTBP [.FALSE.] : INTerpolation of Boundary Potential is used?ZERO [.FALSE.] : boundary potential is set to ZERO ? (metallic conductor boundary conditions)FOCUS [.FALSE.] : previous potential is used to set up boundary potential?PBC [.FALSE.] : 3d periodic boundary conditionNPBC [.FALSE.] : supress XY periodic boundary conditions in membrane calculationsNIMGB [0] : use the image atoms for boundary potential in membrane calculation (NIMGB=1 means the 8 nearest image cells) (NIMGB=2 means the 24 nearest image cells, i.e., 2 shells of images)dielectric boundary-specifications::= [SMOOTH] [SWIN real] [REEN]default : the vdW surface is used for the dielectric boundarySMOOth [.FALSE.] : invoke smoothing dielectric boundarySWIN [0.5] : solute-solvent dielectric boundary Smoothing WINdowREEN [.FALSE.] : the molecular (contact+reentrant) surface is created with WATRadius for the dielectric boundaryphysical variable-specifications::= [EPSW real] [EPSP real] [WATR real] [IONR real] [CONC real] [TEMP real] EPSW [80.0] : bulk solvent dielectric constantEPSP [1.0] : protein interior dielectric constantWATR [0.0] : solvent probe radiusIONR [0.0] : ion exclusion radius (Stern layer)CONC [0.0] : salt concentration [moles/liter]TEMP [300.0] : Temperature [K]membrane-specifications:: [TMEMb real] [HTMEmb real] [ZMEMb real] [EPSMreal] [EPSH real] [VMEMB real]TMEMB [0.0] : thickness of membrane (along Z) HTMEMB [0.0] : thickness of headgroup regionZMEMB [0.0] : membrane position (along Z)EPSM [1.0] : membrane dielectric constantEPSH [EPSM] : membrane headgroup dielectric constant (optional)VMEMB [0.0] : potential difference across membrane (entered in [volts])spherical droplet-spec.::= [DROPlet real] [EPSD real] [XDROplet real] [YDROplet real] [ZDROplet real] [DTOM] [DKAP]DROPlet [0.0] : radius of spherical dropletEPSD [1.0] : dielectric constant of spherical dropletXDROp [0.0] : position of spherical