___________________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 Mon May 16 2011 at 14:02:13 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: 290 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 : 541.9802 centred at (gu) : 88.75766 87.75800 89.95914 assigned negative charge : -539.9820 centred at (gu) : 88.76453 87.70077 89.92763 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7880 nv = 96 ne = 84 npr = 75514 no. pairs analyzed = 75514 no. exposed pairs = 4085 no. arc points = 28552 no. surface atoms = 1382 nbur = 2156 mkacc time = 0.2000000 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= 353 mr = 4367 m= 0 mr = 26 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4200000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2978 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5807031E-10 1.9969391E-09 midg,1,midg; midg,igrid,midg -2.7723228E-09 1.8319061E-09 1,midg,midg; igrid,midg,midg 1.3479823E-09 3.4936401E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 14:02:15 rms-change max change #iterations 0.1195026 17.59689 at 10iterations 1.0001892E-02 1.449917 at 20iterations 8.3831133E-04 0.1197729 at 30iterations 7.3014868E-05 9.9582672E-03 at 40iterations 7.7252998E-06 1.0719299E-03 at 50iterations finished qdiffx linear iterations at : 14:02:18 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 7.7252998E-06 1.0719299E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 14:02:18 3.931u 0.348s 0:05.48 77.9% 0+0k 0+46088io 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 Mon May 16 2011 at 14:02:19 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: 290 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 : 541.9802 centred at (gu) : 86.27234 83.27318 89.87669 assigned negative charge : -539.9820 centred at (gu) : 86.29326 83.10184 89.78269 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 29515 mr = 61879 m= 3712 mr = 21454 m= 139 mr = 2125 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 0.7300000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 26407 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 -2.1958720E-02 -4.8866183E-03 midg,1,midg; midg,igrid,midg -5.4011638E-03 1.1845919E-02 1,midg,midg; igrid,midg,midg 2.9428916E-02 2.9209750E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 1.020000 now iterating at: 14:02:20 rms-change max change #iterations 4.463327 159.5049 at 10iterations 2.027817 65.03340 at 20iterations 0.9170496 27.95135 at 30iterations 0.4184850 12.66913 at 40iterations 0.1894504 5.807631 at 50iterations 8.6140074E-02 2.523616 at 60iterations 3.9077260E-02 1.181538 at 70iterations 1.7763656E-02 0.6746559 at 80iterations 8.0742268E-03 0.2572136 at 90iterations 3.6709758E-03 0.1318398 at 100iterations 1.6700310E-03 5.1452637E-02 at 110iterations 7.6186843E-04 2.5717735E-02 at 120iterations finished qdiffx linear iterations at : 14:02:28 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 7.6186843E-04 2.5717735E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.070000 DelPhi exited at 14:02:29 9.070u 0.374s 0:10.31 91.5% 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 Mon May 16 2011 at 14:02:29 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: 290 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: 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 : 541.9802 centred at (gu) : 84.40823 79.90942 89.81486 assigned negative charge : -539.9820 centred at (gu) : 84.43987 79.65258 89.67378 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 202796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 99417 mr = 149838 m= 31759 mr = 81234 m= 6154 mr = 24945 m= 604 mr = 4496 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 1.820000 number of dielectric boundary points 79877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.970000 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 -0.2898201 -5.6280401E-02 midg,1,midg; midg,igrid,midg -0.2630279 5.4526445E-02 1,midg,midg; igrid,midg,midg 0.3659656 0.3764149 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.140000 now iterating at: 14:02:32 rms-change max change #iterations 10.80611 306.6192 at 10iterations 6.275269 161.1487 at 20iterations 3.617418 71.62592 at 30iterations 2.084481 40.43101 at 40iterations 1.196525 22.62562 at 50iterations 0.6860071 14.16231 at 60iterations 0.3934265 7.628458 at 70iterations 0.2254103 3.889227 at 80iterations 0.1288774 2.163834 at 90iterations 7.3689334E-02 1.286507 at 100iterations 4.2069294E-02 0.7678146 at 110iterations 2.4078805E-02 0.4313779 at 120iterations 1.3768171E-02 0.2445841 at 130iterations 7.8799436E-03 0.1570244 at 140iterations 4.5053284E-03 8.2176208E-02 at 150iterations 2.5731502E-03 4.5577765E-02 at 160iterations 1.4753420E-03 2.4076462E-02 at 170iterations 8.4949646E-04 1.6351700E-02 at 180iterations finished qdiffx linear iterations at : 14:02:45 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 8.4949646E-04 1.6351700E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 14:02:46 15.408u 0.449s 0:16.66 95.0% 0+0k 0+45392io 0pf+0w