___________________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 Wed Sep 30 2009 at 19:22:33 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.2822 centred at (gu) : 88.75232 87.75729 89.95934 assigned negative charge : -539.2841 centred at (gu) : 88.75890 87.70036 89.92802 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7877 nv = 96 ne = 84 npr = 75543 no. pairs analyzed = 75543 no. exposed pairs = 4078 no. arc points = 28533 no. surface atoms = 1378 nbur = 2163 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= 354 mr = 4365 m= 0 mr = 26 time to grow re-entrant surface = 0.2200000 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= 2979 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10288 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4863325E-10 1.9874424E-09 midg,1,midg; midg,igrid,midg -2.7464875E-09 1.8223337E-09 1,midg,midg; igrid,midg,midg 1.3329085E-09 3.5790093E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 19:22:34 rms-change max change #iterations 0.1192307 17.59679 at 10iterations 9.9730799E-03 1.442455 at 20iterations 8.3641621E-04 0.1199121 at 30iterations 7.3151612E-05 9.8876953E-03 at 40iterations 7.8962503E-06 1.1024475E-03 at 50iterations finished qdiffx linear iterations at : 19:22:38 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 7.8962503E-06 1.1024475E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 19:22:39 3.949u 0.372s 0:05.37 80.2% 0+0k 1960+46096io 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 Wed Sep 30 2009 at 19:22:39 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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: 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.2822 centred at (gu) : 86.25633 83.27103 89.87733 assigned negative charge : -539.2841 centred at (gu) : 86.27638 83.10063 89.78387 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28533 grid for indexing accessible points = 1.400000 m= 29506 mr = 61884 m= 3709 mr = 21435 m= 139 mr = 2127 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 0.7100000 number of dielectric boundary points 35464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 26430 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 -2.1927502E-02 -5.0382768E-03 midg,1,midg; midg,igrid,midg -5.3481520E-03 1.1884293E-02 1,midg,midg; igrid,midg,midg 2.9474923E-02 2.9571364E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 19:22:40 rms-change max change #iterations 4.449783 152.0199 at 10iterations 2.022230 65.03767 at 20iterations 0.9142791 27.62250 at 30iterations 0.4170422 12.62866 at 40iterations 0.1888581 5.815741 at 50iterations 8.5867219E-02 2.573658 at 60iterations 3.8982209E-02 1.133789 at 70iterations 1.7701777E-02 0.6365261 at 80iterations 8.0483044E-03 0.2474451 at 90iterations 3.6596251E-03 0.1264381 at 100iterations 1.6643653E-03 5.4878235E-02 at 110iterations 7.5977552E-04 2.5762558E-02 at 120iterations finished qdiffx linear iterations at : 19:22:48 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 7.5977552E-04 2.5762558E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.000000 DelPhi exited at 19:22:49 9.003u 0.440s 0:10.00 94.4% 0+0k 0+45392io 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 Wed Sep 30 2009 at 19:22:49 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.2822 centred at (gu) : 84.38422 79.90622 89.81583 assigned negative charge : -539.2841 centred at (gu) : 84.41457 79.65079 89.67555 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28533 grid for indexing accessible points = 1.400000 m= 99365 mr = 149825 m= 31763 mr = 81209 m= 6155 mr = 24928 m= 604 mr = 4494 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 79828 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 27134 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 -0.2895088 -5.7820980E-02 midg,1,midg; midg,igrid,midg -0.2621391 5.4893013E-02 1,midg,midg; igrid,midg,midg 0.3666505 0.3838517 gauss-seidel spectral radius is 0.9992430 estimated iterations to convergence 287 setup time was (sec) 2.140000 now iterating at: 19:22:51 rms-change max change #iterations 10.77084 306.5934 at 10iterations 6.253275 159.4014 at 20iterations 3.606037 69.62022 at 30iterations 2.077060 40.37136 at 40iterations 1.192491 23.52882 at 50iterations 0.6838045 13.20407 at 60iterations 0.3920268 7.519445 at 70iterations 0.2246231 3.834904 at 80iterations 0.1284305 2.276169 at 90iterations 7.3473290E-02 1.266319 at 100iterations 4.1915067E-02 0.7394085 at 110iterations 2.3989677E-02 0.4353995 at 120iterations 1.3724635E-02 0.2400498 at 130iterations 7.8519005E-03 0.1516342 at 140iterations 4.4894814E-03 7.7188492E-02 at 150iterations 2.5639385E-03 4.4947624E-02 at 160iterations 1.4704308E-03 2.5243282E-02 at 170iterations 8.4652641E-04 1.6410828E-02 at 180iterations finished qdiffx linear iterations at : 19:23:05 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 8.4652641E-04 1.6410828E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 19:23:06 15.599u 0.468s 0:17.70 90.6% 0+0k 0+45400io 0pf+0w