___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Sep 29 2009 at 17:18:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5932345 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 0.5932345 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000014 assigned positive charge : 540.2483 centred at (gu) : 88.74255 87.75110 89.96076 assigned negative charge : -538.2501 centred at (gu) : 88.74810 87.69318 89.92844 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 74698 no. pairs analyzed = 74698 no. exposed pairs = 4093 no. arc points = 28513 no. surface atoms = 1383 nbur = 2155 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 354 mr = 4359 m= 0 mr = 26 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4100000 number of dielectric boundary points 3837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2969 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8555899E-10 2.0271809E-09 midg,1,midg; midg,igrid,midg -2.8093587E-09 1.8416957E-09 1,midg,midg; igrid,midg,midg 1.2812975E-09 3.9007314E-10 gauss-seidel spectral radius is 0.9853630 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 17:18:10 rms-change max change #iterations 0.1194897 17.59708 at 10iterations 9.9972207E-03 1.455624 at 20iterations 8.3479466E-04 0.1209736 at 30iterations 7.0510774E-05 9.5529556E-03 at 40iterations 6.6115235E-06 8.8882446E-04 at 50iterations finished qdiffx linear iterations at : 17:18:13 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 6.6115235E-06 8.8882446E-04 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 17:18:13 3.909u 0.393s 0:05.06 84.7% 0+0k 1944+46080io 3pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Sep 29 2009 at 17:18:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.779703 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 1.779703 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000014 assigned positive charge : 540.2483 centred at (gu) : 86.22704 83.25249 89.88161 assigned negative charge : -538.2501 centred at (gu) : 86.24397 83.07906 89.78512 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28513 grid for indexing accessible points = 1.400000 m= 29472 mr = 61860 m= 3712 mr = 21395 m= 141 mr = 2131 m= 0 mr = 29 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7200000 number of dielectric boundary points 35416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 26405 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5932345 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2735471E-02 -5.3807627E-03 midg,1,midg; midg,igrid,midg -5.4449998E-03 1.2107666E-02 1,midg,midg; igrid,midg,midg 2.9455487E-02 3.0418463E-02 gauss-seidel spectral radius is 0.9985187 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 17:18:15 rms-change max change #iterations 4.446213 152.0131 at 10iterations 2.018300 66.68481 at 20iterations 0.9131982 27.81678 at 30iterations 0.4160439 12.59398 at 40iterations 0.1885266 5.781567 at 50iterations 8.5714728E-02 2.672226 at 60iterations 3.8880322E-02 1.133142 at 70iterations 1.7691744E-02 0.6414719 at 80iterations 8.0436831E-03 0.2505417 at 90iterations 3.6550525E-03 0.1209869 at 100iterations 1.6606906E-03 5.0952911E-02 at 110iterations 7.5853645E-04 2.4915695E-02 at 120iterations finished qdiffx linear iterations at : 17:18:23 total time elapsed so far: 8.980000 # loops : 120 mean,max change (kT/e) : 7.5853645E-04 2.4915695E-02 energy calculations done at 8.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 17:18:24 9.171u 0.424s 0:10.18 94.2% 0+0k 0+45384io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Sep 29 2009 at 17:18:24 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.669555 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 2.669555 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000014 assigned positive charge : 540.2483 centred at (gu) : 84.34026 79.87839 89.82223 assigned negative charge : -538.2501 centred at (gu) : 84.36594 79.61845 89.67743 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28513 grid for indexing accessible points = 1.400000 m= 99273 mr = 149839 m= 31732 mr = 81090 m= 6188 mr = 24914 m= 608 mr = 4506 m= 7 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.840000 number of dielectric boundary points 79749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 27110 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.779703 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3000769 -6.0745589E-02 midg,1,midg; midg,igrid,midg -0.2632182 5.7690728E-02 1,midg,midg; igrid,midg,midg 0.3669092 0.3964678 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.150000 now iterating at: 17:18:27 rms-change max change #iterations 10.75740 306.4907 at 10iterations 6.243604 137.7153 at 20iterations 3.603779 70.38348 at 30iterations 2.075815 43.68657 at 40iterations 1.191211 22.75559 at 50iterations 0.6835344 13.81457 at 60iterations 0.3919983 7.996017 at 70iterations 0.2245585 4.055855 at 80iterations 0.1284096 2.264570 at 90iterations 7.3429398E-02 1.334572 at 100iterations 4.1927405E-02 0.7354164 at 110iterations 2.3980370E-02 0.4129024 at 120iterations 1.3722009E-02 0.2376814 at 130iterations 7.8476304E-03 0.1345596 at 140iterations 4.4867345E-03 7.6426506E-02 at 150iterations 2.5594751E-03 4.6556473E-02 at 160iterations 1.4673594E-03 2.6710510E-02 at 170iterations 8.4457611E-04 1.5862942E-02 at 180iterations finished qdiffx linear iterations at : 17:18:39 total time elapsed so far: 15.04000 # loops : 180 mean,max change (kT/e) : 8.4457611E-04 1.5862942E-02 energy calculations done at 15.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.20000 DelPhi exited at 17:18:40 15.203u 0.507s 0:16.43 95.5% 0+0k 0+45392io 0pf+0w