---------------------------------------------------------------------- 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 . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl 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 Oct 21 2010 at 10:49:41 Parsing input file trans.apbs.in... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from /net/lutefisk/slars/groel_md/1XCK/analysis/24_browdye/trans.pqr. 54845 atoms Centered at (2.924e+00, 8.159e+00, 1.345e+01) Net charge -1.26e+02 e Preparing to run 2 PBE calculations. ---------------------------------------- CALCULATION #1: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.98362 A Current memory usage: 5641.950 MB total, 5641.950 MB high water Using cubic spline charge discretization. Grid dimensions: 353 x 193 x 353 Grid spacings: 0.721 x 0.716 x 0.718 Grid lengths: 253.798 x 137.535 x 252.833 Grid center: (2.975, 8.259, 13.450) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 4 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 1.800 A-radius, -1.000 e-charge, 0.150 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Solving PDE (see io.mc* for details)... Calculating energy (see io.mc* for details)... Calculating forces... ---------------------------------------- CALCULATION #2: MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.98362 A Current memory usage: 5641.950 MB total, 5782.155 MB high water Using cubic spline charge discretization. Grid dimensions: 353 x 193 x 353 Grid spacings: 0.481 x 0.526 x 0.479 Grid lengths: 169.293 x 100.903 x 168.725 Grid center: (2.975, 8.259, 13.450) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 4 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 1.800 A-radius, -1.000 e-charge, 0.150 M concentration 2.000 A-radius, 2.000 e-charge, 0.000 M concentration 2.000 A-radius, -2.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 310.000 K Potential to be written to pymol-generated.dx Solving PDE (see io.mc* for details)... Calculating energy (see io.mc* for details)... Calculating forces... Writing potential to pymol-generated.dx ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 5782.155 MB high water Thanks for using APBS!