Re: [Apbs-users] Question on Boundary Conditions

[Nathan B. <ba...@bi...>]

Hello --

Thanks for all the information; it makes answering your question much 
easier!

It seems to me that differences in energies for the rotated structures 
are probably due to fine grid spacings.  You might try to reduce this 
spacing to below 0.5 A (it's ~ 0.6 A right now?) and see if this 
eliminates or reduces the error.  Energies calculated with discontinuous 
surfaces (e.g., srfm smol) can be very sensitive to grid positions for 
all but the finest grid spacings.

-- Nathan

vin...@dr... wrote, On 3/8/2005 7:19 PM:
> Hi ---
> 
> I've been using APBS to calculate the interaction energy between two 
> pieces of DNA, call them A and B. To do so, I've had APBS calculate the 
> energy of the complex AB, and A,B individually and then defined the 
> interaction energy to be I = E(AB) - E(A) - E(B).
> 
> The goal of the project is the calculate this interaction energy for an 
> ensemble of complexes AB where the orientations of A, B are varied.
> 
> Before running my scripts on my entire ensemble, I've been trying to 
> test out different boundary conditions since the energies will depend on 
> the cglen parameter. As a check of my conditions, I expect the following:
> 
>  - It seems to me that for large values cglen, the interaction energy 
> shouldn't change much when I vary cglen.
> 
>  - It also seems to me that if I apply a rigid rotation to AB, A, and B 
> and then recalculate the interaction energy, this should also tend to a 
> limiting value as I increase cglen for large values of cglen.
> 
>  - Furthermore, the interaction energy between AB should be the same as 
> the interaction energy I calculate for the rotated AB system for large 
> cglen --- afterall, they're the same molecule, just rotated in space.
> 
> However, when I did this test, I found that the first two were observed 
> (that is, both unrotated and rotated energies stopped changing as I 
> varied cglen for large cglen). However, the interaction energies I 
> calculated differed between the rotated/unrotated systems by about 4%. 
> The cglen I used were large (each cglen dimension was up to 6x the 
> typical molecular dimension).
> 
> Although the discrepency isn't huge, I'd like to understand the origin 
> of it in case I'll need to split hairs in the future. Anybody else have 
> this problem or can help explain it to me? Perhaps I've misunderstood 
> the meaning of cglen, fglen, and the dime arguments ..
> 
> Thanks,
> 
> Vince
> 
> PS -- attached below are the outputs of psize.py and the .in files
> 
> psize.py output for AB complex
> ################# MOLECULE INFO ####################
> Number of ATOM entries = 1516
> Number of HETATM entries (ignored) = 0
> Total charge = -44.000 e
> Dimensions = 44.210 x 41.008 x 65.643 A
> Center = 12.138 x -8.546 x 30.084 A
> Lower corner = -9.967 x -29.050 x -2.737 A
> Upper corner = 34.243 x 11.958 x 62.906 A
> 
> ############## GENERAL CALCULATION INFO #############
> Coarse grid dims = 75.157 x 69.714 x 111.593 A
> Fine grid dims = 64.210 x 61.008 x 85.643 A
> Num. fine grid pts. = 97 x 97 x 161
> Fine mesh spacing = 0.668854 x 0.6355 x 0.535269 A
> Estimated mem. required for sequential solve = 231.148 MB
> Number of focusing operations = 2
> 
> psize.py output for rotated AB complex
> ################# MOLECULE INFO ####################
> Number of ATOM entries = 1516
> Number of HETATM entries (ignored) = 0
> Total charge = -44.000 e
> Dimensions = 66.155 x 41.008 x 50.193 A
> Center = 28.367 x -8.546 x 23.087 A
> Lower corner = -4.711 x -29.050 x -2.010 A
> Upper corner = 61.444 x 11.958 x 48.183 A
> 
> ############## GENERAL CALCULATION INFO #############
> Coarse grid dims = 112.463 x 69.714 x 85.327 A
> Fine grid dims = 86.155 x 61.008 x 70.192 A
> Num. fine grid pts. = 161 x 97 x 129
> Fine mesh spacing = 0.538467 x 0.6355 x 0.548379 A
> Estimated mem. required for sequential solve = 307.402 MB
> Number of focusing operations = 2
> 
> 
> read
>     mol pqr duplexA.pqr
>     mol pqr B0600.pqr
>     mol pqr A+B0600.pqr
>     mol pqr rot_duplexA.pqr
>     mol pqr rot_B0600.pqr
>     mol pqr rot_A+B0600.pqr
> end
> 
> elec name duplexA
>     mg-auto
>     dime 97 97 161
>     cglen 300 300 300
>     fglen 64.210 61.008 85.643
>     Cgcent 12.138 -8.546 30.084
>     fgcent 12.138 -8.546 30.084
>     mol 1
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> elec name B0600
>     mg-auto
>     dime 97 97 161
>     cglen 300 300 300
>     fglen 64.210 61.008 85.643
>     Cgcent 12.138 -8.546 30.084
>     fgcent 12.138 -8.546 30.084
>     mol 2
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> elec name A+B
>     mg-auto
>     dime 97 97 161
>     cglen 300 300 300
>     fglen 64.210 61.008 85.643
>     Cgcent 12.138 -8.546 30.084
>     fgcent 12.138 -8.546 30.084
>     mol 3
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> elec name rot_duplexA
>     mg-auto
>     dime 161 97 129
>     cglen 300 300 300
>     fglen 86.155 61.008 70.192
>     Cgcent 28.367 -8.546 23.087
>     fgcent 28.367 -8.546 23.087
>     mol 4
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> elec name rot_B0600
>     mg-auto
>     dime 161 97 129
>     cglen 300 300 300
>     fglen 86.155 61.008 70.192
>     Cgcent 28.367 -8.546 23.087
>     fgcent 28.367 -8.546 23.087
>     mol 5
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> elec name rot_A+B
>     mg-auto
>     dime 161 97 129
>     cglen 300 300 300
>     fglen 86.155 61.008 70.192
>     Cgcent 28.367 -8.546 23.087
>     fgcent 28.367 -8.546 23.087
>     mol 6
>     npbe
>     bcfl sdh
>     ion 1 0.150 2.0
>     ion -1 0.150 2.0
>     pdie 2.0
>     sdie 78.54
>     srfm smol
>     chgm spl2
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy total
>     calcforce no
> end
> 
> print energy duplexA end
> print energy B0600 end
> print energy A+B end
> print energy A+B - duplexA -  B0600 end
> print energy rot_duplexA end
> print energy rot_B0600 end
> print energy rot_A+B end
> print energy rot_A+B - rot_duplexA - rot_B0600 end
> 
> quit
> 
> Results of the Calculation:
> 
> 
>     ----------------------------------------------------------------------
>     APBS -- Adaptive Poisson-Boltzmann Solver
>     Version 0.3.2
> 
>     Nathan A. Baker (ba...@bi...)
>     Dept. Biochemistry and Molecular Biophysics
>     Center for Computational Biology
>     Washington University in St. Louis
> 
>     Additional contributing authors listed in the code documentation.
> 
>     Copyright (c) 2002-2004.  Washington University in St. Louis.
>     All Rights Reserved.
>     Portions Copyright (c) 1999-2002.  The Regents of the University of
>     California.
>     Portions Copyright (c) 1995.  Michael Holst.
> 
>     This program is free software; you can redistribute it and/or modify
>     it under the terms of the GNU General Public License as published by
>     the Free Software Foundation; either version 2 of the License, or
>     (at your option) any later version.
> 
>     This program is distributed in the hope that it will be useful,
>     but WITHOUT ANY WARRANTY; without even the implied warranty of
>     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
>     GNU General Public License for more details.
> 
>     You should have received a copy of the GNU General Public License
>     along with this program; if not, write to the Free Software
>     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
> USA
>     ----------------------------------------------------------------------
>     APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation
>     numerically.  FEtk and PMG are developed and maintained by the Holst
>     Research Group at UC San Diego.  PMG is designed to solve the nonlinear
>     Poisson-Boltzmann equation and similar problems with linear space and
>     time complexity through the use of box methods, inexact Newton methods,
>     and algebraic multilevel methods.  FEtk is designed to solve general
>     coupled systems of nonlinear partial differential equations accurately
>     and efficiently using adaptive multilevel finite element methods,
>     inexact Newton methods, and algebraic multilevel methods.  More
>     information about PMG and FEtk may be found at <http://www.FEtk.ORG>.
>     ----------------------------------------------------------------------
> 
> 
> This executable compiled on Mar  7 2005 at 17:49:38
> 
> Parsing input file params300...
> Parsed input file.
> Got PQR paths for 6 molecules
> Reading PQR-format atom data from duplexA.pqr.
>   759 atoms
>   Centered at (1.003e+00, 5.900e-01, 1.818e+01)
>   Net charge -2.20e+01 e
> Reading PQR-format atom data from B0600.pqr.
>   757 atoms
>   Centered at (1.263e+01, -1.169e+01, 5.126e+01)
>   Net charge -2.20e+01 e
> Reading PQR-format atom data from A+B0600.pqr.
>   1516 atoms
>   Centered at (1.214e+01, -8.546e+00, 3.008e+01)
>   Net charge -4.40e+01 e
> Reading PQR-format atom data from rot_duplexA.pqr.
>   759 atoms
>   Centered at (1.246e+01, 5.900e-01, 1.476e+01)
>   Net charge -2.20e+01 e
> Reading PQR-format atom data from rot_B0600.pqr.
>   757 atoms
>   Centered at (4.570e+01, -1.169e+01, 2.917e+01)
>   Net charge -2.20e+01 e
> Reading PQR-format atom data from rot_A+B0600.pqr.
>   1516 atoms
>   Centered at (2.837e+01, -8.546e+00, 2.309e+01)
>   Net charge -4.40e+01 e
> Preparing to run 18 PBE calculations.
> ----------------------------------------
> CALCULATION #1 (duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  283.274 MB total, 283.274 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 3.125 x 3.125 x 1.875
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 6.620052051897E+02 kJ/mol
> ----------------------------------------
> CALCULATION #2 (duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  282.022 MB total, 294.409 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 1.446 x 1.409 x 1.002
>   Grid lengths: 138.791 x 135.286 x 160.290
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 8.505506220802E+03 kJ/mol
> ----------------------------------------
> CALCULATION #3 (duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  282.022 MB total, 294.409 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 0.669 x 0.636 x 0.535
>   Grid lengths: 64.210 x 61.008 x 85.643
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 6.190766600855E+04 kJ/mol
> ----------------------------------------
> CALCULATION #4 (B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  284.673 MB total, 294.409 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 3.125 x 3.125 x 1.875
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 7.337998367409E+02 kJ/mol
> ----------------------------------------
> CALCULATION #5 (B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  283.628 MB total, 297.413 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 1.446 x 1.409 x 1.002
>   Grid lengths: 138.791 x 135.286 x 160.290
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 9.380279796394E+03 kJ/mol
> ----------------------------------------
> CALCULATION #6 (B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  283.628 MB total, 297.413 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 0.669 x 0.636 x 0.535
>   Grid lengths: 64.210 x 61.008 x 85.643
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 6.307103446694E+04 kJ/mol
> ----------------------------------------
> CALCULATION #7 (A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  288.407 MB total, 298.047 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 3.125 x 3.125 x 1.875
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.403216167215E+03 kJ/mol
> ----------------------------------------
> CALCULATION #8 (A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  287.385 MB total, 304.905 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 1.446 x 1.409 x 1.002
>   Grid lengths: 138.791 x 135.286 x 160.290
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.789400456442E+04 kJ/mol
> ----------------------------------------
> CALCULATION #9 (A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  287.385 MB total, 304.905 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 97 x 97 x 161
>   Grid spacings: 0.669 x 0.636 x 0.535
>   Grid lengths: 64.210 x 61.008 x 85.643
>   Grid center: (12.138, -8.546, 30.084)
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.249868998221E+05 kJ/mol
> ----------------------------------------
> CALCULATION #10 (rot_duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  374.818 MB total, 388.214 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.875 x 3.125 x 2.344
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 4
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 8.681043936483E+02 kJ/mol
> ----------------------------------------
> CALCULATION #11 (rot_duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  373.594 MB total, 388.750 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.005 x 1.409 x 1.134
>   Grid lengths: 160.768 x 135.286 x 145.112
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 4
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.197050024673E+04 kJ/mol
> ----------------------------------------
> CALCULATION #12 (rot_duplexA): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  373.594 MB total, 388.750 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 0.538 x 0.636 x 0.548
>   Grid lengths: 86.155 x 61.008 x 70.192
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 4
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 6.951353375660E+04 kJ/mol
> ----------------------------------------
> CALCULATION #13 (rot_B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  376.017 MB total, 388.750 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.875 x 3.125 x 2.344
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 5
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 8.977977013796E+02 kJ/mol
> ----------------------------------------
> CALCULATION #14 (rot_B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  374.975 MB total, 391.329 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.005 x 1.409 x 1.134
>   Grid lengths: 160.768 x 135.286 x 145.112
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 5
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.197209089208E+04 kJ/mol
> ----------------------------------------
> CALCULATION #15 (rot_B0600): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  374.975 MB total, 391.329 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 0.538 x 0.636 x 0.548
>   Grid lengths: 86.155 x 61.008 x 70.192
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 5
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 7.081571617844E+04 kJ/mol
> ----------------------------------------
> CALCULATION #16 (rot_A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  376.960 MB total, 391.329 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.875 x 3.125 x 2.344
>   Grid lengths: 300.000 x 300.000 x 300.000
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 6
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.774984364767E+03 kJ/mol
> ----------------------------------------
> CALCULATION #17 (rot_A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  376.212 MB total, 393.510 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 1.005 x 1.409 x 1.134
>   Grid lengths: 160.768 x 135.286 x 145.112
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 6
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 2.395102633008E+04 kJ/mol
> ----------------------------------------
> CALCULATION #18 (rot_A+B): MULTIGRID
>   Setting up problem...
>   Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
>   Debye length:  7.8566 A
>   Current memory usage:  376.212 MB total, 393.510 MB high water
>   Using cubic spline charge discretization.
>   Grid dimensions: 161 x 97 x 129
>   Grid spacings: 0.538 x 0.636 x 0.548
>   Grid lengths: 86.155 x 61.008 x 70.192
>   Grid center: (28.367, -8.546, 23.087)
>   Multigrid levels: 4
>   Molecule ID: 6
>   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: 78.540
>   Using "molecular" surface definition; harmonic average smoothing
>   Solvent probe radius: 1.400 A
>   Temperature:  298.150 K
>   Surface tension:  0.105 kJ/mol/A^2
>   Electrostatic energies will be calculated
>   Solving PDE (see io.mc* for details)...
>   Total electrostatic energy = 1.403377945210E+05 kJ/mol
> ----------------------------------------
> PRINT STATEMENTS
> print energy 1 (duplexA) end
>   Local net energy (PE 0) = 6.190766600855E+04 kJ/mol
>   Global net energy = 6.190766600855E+04 kJ/mol
> print energy 2 (B0600) end
>   Local net energy (PE 0) = 6.307103446694E+04 kJ/mol
>   Global net energy = 6.307103446694E+04 kJ/mol
> print energy 3 (A+B) end
>   Local net energy (PE 0) = 1.249868998221E+05 kJ/mol
>   Global net energy = 1.249868998221E+05 kJ/mol
> print energy 3 (A+B) - 1 (duplexA) - 2 (B0600) end
>   Local net energy (PE 0) = 8.199346623975E+00 kJ/mol
>   Global net energy = 8.199346623975E+00 kJ/mol
> print energy 4 (rot_duplexA) end
>   Local net energy (PE 0) = 6.951353375660E+04 kJ/mol
>   Global net energy = 6.951353375660E+04 kJ/mol
> print energy 5 (rot_B0600) end
>   Local net energy (PE 0) = 7.081571617844E+04 kJ/mol
>   Global net energy = 7.081571617844E+04 kJ/mol
> print energy 6 (rot_A+B) end
>   Local net energy (PE 0) = 1.403377945210E+05 kJ/mol
>   Global net energy = 1.403377945210E+05 kJ/mol
> print energy 6 (rot_A+B) - 4 (rot_duplexA) - 5 (rot_B0600) end
>   Local net energy (PE 0) = 8.544586008344E+00 kJ/mol
>   Global net energy = 8.544586008344E+00 kJ/mol
> ----------------------------------------
> CLEANING UP AND SHUTTING DOWN...
> Destroying force arrays.
> No energy arrays to destroy.
> Destroying multigrid structures.
> Destroying 6 molecules
> Final memory usage:  0.000 MB total, 393.510 MB high water
> 
> 
> Thanks for using APBS!
> 
> 
> _______________________________________________
> apbs-users mailing list
> apb...@ch...
> http://cholla.wustl.edu/mailman/listinfo/apbs-users

-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker