___________________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 Fri Sep 18 2009 at 15:52:16 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 : 2.000005 assigned positive charge : 538.6483 centred at (gu) : 88.73242 87.74290 89.95646 assigned negative charge : -536.6500 centred at (gu) : 88.74094 87.68509 89.92440 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 74698 no. pairs analyzed = 74698 no. exposed pairs = 4094 no. arc points = 28517 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 = 0.2200000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4200000 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 10279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7289046E-10 2.0088526E-09 midg,1,midg; midg,igrid,midg -2.7978053E-09 1.8303659E-09 1,midg,midg; igrid,midg,midg 1.4425710E-09 2.9871555E-10 gauss-seidel spectral radius is 0.9853630 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 15:52:17 rms-change max change #iterations 0.1185723 17.59710 at 10iterations 9.9456953E-03 1.400776 at 20iterations 8.3277689E-04 0.1192894 at 30iterations 7.3767311E-05 9.8857880E-03 at 40iterations 8.5882648E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 15:52:21 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 8.5882648E-06 1.0604858E-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 15:52:21 3.949u 0.373s 0:05.03 85.6% 0+0k 1896+46088io 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 Fri Sep 18 2009 at 15:52:21 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 : 2.000005 assigned positive charge : 538.6483 centred at (gu) : 86.19659 83.22789 89.86866 assigned negative charge : -536.6500 centred at (gu) : 86.22243 83.05479 89.77293 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28517 grid for indexing accessible points = 1.400000 m= 29474 mr = 61862 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 0.7000000 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 0.8400000 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 -2.2535380E-02 -5.4407781E-03 midg,1,midg; midg,igrid,midg -5.3097857E-03 1.2175833E-02 1,midg,midg; igrid,midg,midg 2.9984003E-02 2.9979818E-02 gauss-seidel spectral radius is 0.9985187 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 15:52:23 rms-change max change #iterations 4.425709 152.0131 at 10iterations 2.008938 66.66069 at 20iterations 0.9089094 27.87974 at 30iterations 0.4141045 12.58263 at 40iterations 0.1876768 5.813925 at 50iterations 8.5332572E-02 2.709324 at 60iterations 3.8713802E-02 1.122713 at 70iterations 1.7610675E-02 0.6418610 at 80iterations 8.0091255E-03 0.2507706 at 90iterations 3.6382074E-03 0.1195831 at 100iterations 1.6533588E-03 5.0491333E-02 at 110iterations 7.5566710E-04 2.3921967E-02 at 120iterations finished qdiffx linear iterations at : 15:52:31 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 7.5566710E-04 2.3921967E-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 15:52:32 9.006u 0.422s 0:10.44 90.2% 0+0k 8+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 Fri Sep 18 2009 at 15:52:32 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: 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 : 2.000005 assigned positive charge : 538.6483 centred at (gu) : 84.29462 79.84150 89.80281 assigned negative charge : -536.6500 centred at (gu) : 84.33363 79.58204 89.65913 start vw surface at 0.1800000 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 = 28517 grid for indexing accessible points = 1.400000 m= 99272 mr = 149837 m= 31729 mr = 81087 m= 6189 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 1.830000 number of dielectric boundary points 79751 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 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 -0.2975675 -6.1390225E-02 midg,1,midg; midg,igrid,midg -0.2616597 5.8697022E-02 1,midg,midg; igrid,midg,midg 0.3736666 0.3907720 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.140000 now iterating at: 15:52:34 rms-change max change #iterations 10.71430 306.4906 at 10iterations 6.221321 128.2251 at 20iterations 3.591070 65.36100 at 30iterations 2.068684 42.65678 at 40iterations 1.187121 22.78111 at 50iterations 0.6812512 13.33081 at 60iterations 0.3906519 7.665432 at 70iterations 0.2238497 3.869896 at 80iterations 0.1280077 2.212453 at 90iterations 7.3198706E-02 1.354983 at 100iterations 4.1800193E-02 0.7378197 at 110iterations 2.3909802E-02 0.4120867 at 120iterations 1.3686318E-02 0.2552547 at 130iterations 7.8282058E-03 0.1379814 at 140iterations 4.4780574E-03 7.5294495E-02 at 150iterations 2.5563987E-03 4.6419144E-02 at 160iterations 1.4679134E-03 2.7866364E-02 at 170iterations 8.4696291E-04 1.5839815E-02 at 180iterations finished qdiffx linear iterations at : 15:52:48 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 8.4696291E-04 1.5839815E-02 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 15:52:49 15.347u 0.459s 0:16.74 94.3% 0+0k 0+45392io 0pf+0w