

----------------------------------------------------------------------
	APBS -- Adaptive Poisson-Boltzmann Solver
	Version 1.3
	
	Nathan A. Baker (nathan.baker@pnl.gov)
	Washington University in St. Louis
	
	Additional contributing authors listed in the code documentation.
	
	Copyright (c) 2010, Pacific Northwest National Laboratory.  Portions Copyright (c) 2002-2010, Washington University in St. Louis.  Portions Copyright (c) 2002-2010, Nathan A. Baker.  Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst.
	All rights reserved.
	
	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions are met: 
	
	* Redistributions of source code must retain the above copyright notice, this
	list of conditions and the following disclaimer.  
	
	* Redistributions in binary form must reproduce the above copyright notice,
	this list of conditions and the following disclaimer in the documentation
	and/or other materials provided with the distribution.
	
	* Neither the name of Washington University in St. Louis nor the names of its
	contributors may be used to endorse or promote products derived from this
	software without specific prior written permission.
	
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
	"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------------------------------------------------
	APBS uses FETK (the Finite Element ToolKit) to solve the
	Poisson-Boltzmann equation numerically.  FETK is a portable collection
	of finite element modeling class libraries developed by the Michael Holst
	research group and written in an object-oriented form of C.  FEtk is
	designed to solve general coupled systems of nonlinear partial differential
	equations using adaptive finite element methods, inexact Newton methods,
	and algebraic multilevel methods.  More information about FEtk may be found
	at <http://www.FEtk.ORG>.
----------------------------------------------------------------------
	APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.  
	Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
	which has been modified by Patrice Koehl
	<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
	memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
	Please cite your use of APBS as:

	Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
	nanosystems: application to microtubules and the ribosome. Proc.
	Natl. Acad. Sci. USA 98, 10037-10041 2001.
	

This executable compiled on Jul 15 2019 at 19:36:22

Parsing input file stru10.in...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from comp10.pqr.
  3218 atoms
  Centered at (6.280e+01, 6.280e+01, 2.961e+01)
  Net charge 4.82e+00 e
Reading PQR-format atom data from Protein10.pqr.
  3129 atoms
  Centered at (6.280e+01, 6.280e+01, 2.961e+01)
  Net charge 4.79e+00 e
Reading PQR-format atom data from BEC10.pqr.
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
  89 atoms
  Centered at (6.206e+01, 6.370e+01, 3.066e+01)
  Net charge 3.00e-02 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (comp10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1206.562 MB total, 1206.562 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.250715311202E+05 kJ/mol
  Calculating forces...
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
----------------------------------------
CALCULATION #2 (comp10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1206.562 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 3.012893067145E+05 kJ/mol
  Calculating forces...
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
----------------------------------------
CALCULATION #3 (Protein10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1205.405 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 2
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.226064890318E+05 kJ/mol
  Calculating forces...
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100
----------------------------------------
CALCULATION #4 (Protein10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1205.405 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 2
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 2.955730810762E+05 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #5 (BEC10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1161.324 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 3
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 2.373283902834E+03 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #6 (BEC10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  7.95385 A
  Current memory usage:  1161.324 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 3
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.150 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 80.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 5.639192569465E+03 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #7 (vaccomp10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1206.562 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.349584905192E+05 kJ/mol
  Calculating forces...

focusFillBound:  WARNING! Unusually large potential values
                   detected on the focusing boundary!  
                   Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #8 (vaccomp10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1206.562 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 3.108309942467E+05 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #9 (vacProtein10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1205.405 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 2
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 1.326988094478E+05 kJ/mol
  Calculating forces...

focusFillBound:  WARNING! Unusually large potential values
                   detected on the focusing boundary!  
                   Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #10 (vacProtein10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1205.405 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 2
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 3.053092037514E+05 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #11 (vacBEC10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1161.324 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.526 x 0.668 x 0.575
  Grid lengths: 84.099 x 106.879 x 110.313
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 3
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 2.566384959104E+03 kJ/mol
  Calculating forces...
----------------------------------------
CALCULATION #12 (vacBEC10): MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  1161.324 MB total, 1259.793 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 161 x 161 x 193
  Grid spacings: 0.309 x 0.393 x 0.338
  Grid lengths: 49.470 x 62.870 x 64.890
  Grid center: (62.855, 62.825, 29.645)
  Multigrid levels: 4
  Molecule ID: 3
  Nonlinear traditional PBE
  Boundary conditions from focusing
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 1.000
  Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  300.000 K
  Electrostatic energies will be calculated
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Total electrostatic energy = 5.810442425144E+03 kJ/mol
  Calculating forces...
----------------------------------------
PRINT STATEMENTS

print energy 1 (comp10) - 2 (Protein10) - 3 (BEC10) - 4 (vaccomp10) + 5 (vacProtein10) + 6 (vacBEC10) end
  Local net energy (PE 0) = 3.656849987032E+02 kJ/mol
  Global net ELEC energy = 3.656849987032E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 3 molecules
Final memory usage:  0.001 MB total, 1259.793 MB high water


Thanks for using APBS!

