___________________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 18:34:24 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3532 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 : 3532 total number of charged atoms : 3384 net assigned charge : 2.000014 assigned positive charge : 540.5123 centred at (gu) : 88.74950 87.74530 89.96669 assigned negative charge : -538.5141 centred at (gu) : 88.75665 87.68797 89.93505 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7876 nv = 96 ne = 84 npr = 75398 no. pairs analyzed = 75398 no. exposed pairs = 4110 no. arc points = 28734 no. surface atoms = 1389 nbur = 2143 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 = 4354 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 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2983 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10268 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5842730E-10 2.0015658E-09 midg,1,midg; midg,igrid,midg -2.7767328E-09 1.8251154E-09 1,midg,midg; igrid,midg,midg 1.3646744E-09 3.4069295E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 18:34:25 rms-change max change #iterations 0.1190358 17.59689 at 10iterations 9.9634379E-03 1.422077 at 20iterations 8.4436772E-04 0.1147757 at 30iterations 8.2265120E-05 1.0932922E-02 at 40iterations 1.2528266E-05 1.4991760E-03 at 50iterations finished qdiffx linear iterations at : 18:34:29 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.2528266E-05 1.4991760E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 18:34:30 4.332u 0.498s 0:05.62 85.7% 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 18:34:30 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 = 3532 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 : 3532 total number of charged atoms : 3384 net assigned charge : 2.000014 assigned positive charge : 540.5123 centred at (gu) : 86.24789 83.23507 89.89938 assigned negative charge : -538.5141 centred at (gu) : 86.26962 83.06347 89.80501 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 29471 mr = 61713 m= 3726 mr = 21389 m= 139 mr = 2133 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 0.7400000 number of dielectric boundary points 35588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 26361 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 -2.1692552E-02 -4.9157906E-03 midg,1,midg; midg,igrid,midg -5.4082545E-03 1.1802022E-02 1,midg,midg; igrid,midg,midg 2.9437134E-02 2.9013911E-02 gauss-seidel spectral radius is 0.9985192 estimated iterations to convergence 206 setup time was (sec) 1.050000 now iterating at: 18:34:31 rms-change max change #iterations 4.459978 152.0337 at 10iterations 2.026323 65.04324 at 20iterations 0.9162531 28.16298 at 30iterations 0.4182419 12.67363 at 40iterations 0.1893860 5.867401 at 50iterations 8.6159930E-02 2.567321 at 60iterations 3.9116204E-02 1.105961 at 70iterations 1.7781898E-02 0.6557655 at 80iterations 8.0806604E-03 0.2648869 at 90iterations 3.6761425E-03 0.1266403 at 100iterations 1.6731414E-03 5.1269531E-02 at 110iterations 7.6442509E-04 2.6101112E-02 at 120iterations finished qdiffx linear iterations at : 18:34:41 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 7.6442509E-04 2.6101112E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 18:34:42 9.894u 0.537s 0:12.10 86.1% 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 18:34:42 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 = 3532 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 : 3532 total number of charged atoms : 3384 net assigned charge : 2.000014 assigned positive charge : 540.5123 centred at (gu) : 84.37156 79.85225 89.84888 assigned negative charge : -538.5141 centred at (gu) : 84.40444 79.59505 89.70727 start vw surface at 0.1800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 202578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 99227 mr = 149479 m= 31753 mr = 80972 m= 6182 mr = 24933 m= 606 mr = 4503 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 1.850000 number of dielectric boundary points 80119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 27062 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 -0.2858274 -5.6774728E-02 midg,1,midg; midg,igrid,midg -0.2633918 5.4340333E-02 1,midg,midg; igrid,midg,midg 0.3659344 0.3729846 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.160000 now iterating at: 18:34:45 rms-change max change #iterations 10.80555 306.7223 at 10iterations 6.282440 161.2549 at 20iterations 3.626034 77.23680 at 30iterations 2.092880 42.07468 at 40iterations 1.203300 22.41988 at 50iterations 0.6903992 14.17175 at 60iterations 0.3961202 7.094887 at 70iterations 0.2271656 3.842695 at 80iterations 0.1300061 2.319836 at 90iterations 7.4397564E-02 1.354328 at 100iterations 4.2505167E-02 0.7747436 at 110iterations 2.4358194E-02 0.4514456 at 120iterations 1.3928817E-02 0.2575135 at 130iterations 7.9865083E-03 0.1548109 at 140iterations 4.5731226E-03 7.9892159E-02 at 150iterations 2.6141950E-03 4.5211792E-02 at 160iterations 1.5018567E-03 2.6731491E-02 at 170iterations 8.6688518E-04 1.5592575E-02 at 180iterations finished qdiffx linear iterations at : 18:35:00 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 8.6688518E-04 1.5592575E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 18:35:01 15.982u 0.494s 0:18.68 88.1% 0+0k 0+45392io 0pf+0w