___________________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 13:09:46 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 : 541.4822 centred at (gu) : 88.75525 87.76121 89.96114 assigned negative charge : -539.4841 centred at (gu) : 88.76036 87.70293 89.92934 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7883 nv = 96 ne = 84 npr = 75746 no. pairs analyzed = 75746 no. exposed pairs = 4086 no. arc points = 28557 no. surface atoms = 1379 nbur = 2162 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= 355 mr = 4371 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 3841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2982 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6631522E-10 2.0098241E-09 midg,1,midg; midg,igrid,midg -2.8359162E-09 1.8579032E-09 1,midg,midg; igrid,midg,midg 1.2548853E-09 4.0465647E-10 gauss-seidel spectral radius is 0.9853627 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 13:09:47 rms-change max change #iterations 0.1197417 17.59671 at 10iterations 9.9978978E-03 1.455528 at 20iterations 8.3297561E-04 0.1178818 at 30iterations 7.0289789E-05 9.7780228E-03 at 40iterations 6.4905930E-06 9.2315674E-04 at 50iterations finished qdiffx linear iterations at : 13:09:50 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 6.4905930E-06 9.2315674E-04 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 13:09:51 3.923u 0.430s 0:05.09 85.4% 0+0k 0+46096io 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 13:09:51 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: 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 : 541.4822 centred at (gu) : 86.26513 83.28281 89.88272 assigned negative charge : -539.4841 centred at (gu) : 86.28074 83.10838 89.78788 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28557 grid for indexing accessible points = 1.400000 m= 29506 mr = 61897 m= 3704 mr = 21427 m= 139 mr = 2127 m= 0 mr = 29 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7200000 number of dielectric boundary points 35467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 26429 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 -2.2719715E-02 -5.2478970E-03 midg,1,midg; midg,igrid,midg -5.4157679E-03 1.2181016E-02 1,midg,midg; igrid,midg,midg 2.9421022E-02 3.0201046E-02 gauss-seidel spectral radius is 0.9985188 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 13:09:53 rms-change max change #iterations 4.452169 152.0154 at 10iterations 2.022401 64.98428 at 20iterations 0.9144180 27.83524 at 30iterations 0.4168971 12.60800 at 40iterations 0.1889457 5.846258 at 50iterations 8.5887812E-02 2.796844 at 60iterations 3.9001592E-02 1.152252 at 70iterations 1.7696310E-02 0.6071701 at 80iterations 8.0473358E-03 0.2565994 at 90iterations 3.6568122E-03 0.1286221 at 100iterations 1.6627343E-03 5.2745819E-02 at 110iterations 7.5898465E-04 2.3071289E-02 at 120iterations finished qdiffx linear iterations at : 13:10:01 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 7.5898465E-04 2.3071289E-02 energy calculations done at 8.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 13:10:02 9.047u 0.379s 0:10.59 88.8% 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 13:10:02 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: 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 : 541.4822 centred at (gu) : 84.39741 79.92386 89.82392 assigned negative charge : -539.4841 centred at (gu) : 84.42112 79.66240 89.68157 start vw surface at 0.1800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 202777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28557 grid for indexing accessible points = 1.400000 m= 99387 mr = 149870 m= 31747 mr = 81196 m= 6148 mr = 24911 m= 604 mr = 4491 m= 7 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.840000 number of dielectric boundary points 79855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.990000 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 -0.2996125 -6.0354769E-02 midg,1,midg; midg,igrid,midg -0.2629992 5.9780277E-02 1,midg,midg; igrid,midg,midg 0.3664189 0.3906958 gauss-seidel spectral radius is 0.9992431 estimated iterations to convergence 287 setup time was (sec) 2.150000 now iterating at: 13:10:05 rms-change max change #iterations 10.77059 306.5998 at 10iterations 6.253590 150.6641 at 20iterations 3.606352 69.81647 at 30iterations 2.076874 43.47831 at 40iterations 1.192477 23.03440 at 50iterations 0.6835623 12.19044 at 60iterations 0.3919534 8.732666 at 70iterations 0.2245517 4.155178 at 80iterations 0.1284214 2.357590 at 90iterations 7.3489472E-02 1.264700 at 100iterations 4.1928478E-02 0.7036667 at 110iterations 2.3989297E-02 0.4157276 at 120iterations 1.3721192E-02 0.2584438 at 130iterations 7.8493292E-03 0.1554031 at 140iterations 4.4849706E-03 7.6925278E-02 at 150iterations 2.5617022E-03 4.1872978E-02 at 160iterations 1.4681271E-03 2.4311066E-02 at 170iterations 8.4458257E-04 1.5569687E-02 at 180iterations finished qdiffx linear iterations at : 13:10:19 total time elapsed so far: 15.18000 # loops : 180 mean,max change (kT/e) : 8.4458257E-04 1.5569687E-02 energy calculations done at 15.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 13:10:20 15.350u 0.492s 0:17.59 90.0% 0+0k 0+45400io 0pf+0w