___________________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 16:16:53 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) : 88.75364 87.75860 89.96103 assigned negative charge : -539.2841 centred at (gu) : 88.75909 87.70058 89.92773 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7879 nv = 96 ne = 84 npr = 75548 no. pairs analyzed = 75548 no. exposed pairs = 4079 no. arc points = 28531 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 = 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 0.4300000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2981 ## 359 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2799699E-10 2.0687803E-09 midg,1,midg; midg,igrid,midg -2.8189415E-09 1.8501112E-09 1,midg,midg; igrid,midg,midg 1.2735326E-09 3.9381609E-10 gauss-seidel spectral radius is 0.9853627 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 16:16:54 rms-change max change #iterations 0.1195757 17.59671 at 10iterations 9.9677471E-03 1.461227 at 20iterations 8.3318615E-04 0.1190624 at 30iterations 7.0318369E-05 9.7007751E-03 at 40iterations 6.5278045E-06 9.7274780E-04 at 50iterations finished qdiffx linear iterations at : 16:16:57 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 6.5278045E-06 9.7274780E-04 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 16:16:57 3.931u 0.359s 0:04.99 85.7% 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 16:16:58 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 : 541.2822 centred at (gu) : 86.26027 83.27494 89.88239 assigned negative charge : -539.2841 centred at (gu) : 86.27693 83.10131 89.78303 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 grid for indexing accessible points = 1.400000 m= 29512 mr = 61923 m= 3711 mr = 21446 m= 139 mr = 2126 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 35454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 26433 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 -2.2876648E-02 -4.8683155E-03 midg,1,midg; midg,igrid,midg -5.4100351E-03 1.2097120E-02 1,midg,midg; igrid,midg,midg 2.9464185E-02 3.0140812E-02 gauss-seidel spectral radius is 0.9985188 estimated iterations to convergence 206 setup time was (sec) 1.030000 now iterating at: 16:16:59 rms-change max change #iterations 4.450271 152.0177 at 10iterations 2.022191 65.03563 at 20iterations 0.9142517 27.64824 at 30iterations 0.4168589 12.62798 at 40iterations 0.1889034 5.827386 at 50iterations 8.5876711E-02 2.617340 at 60iterations 3.8997475E-02 1.167816 at 70iterations 1.7694769E-02 0.6123371 at 80iterations 8.0523388E-03 0.2538786 at 90iterations 3.6588500E-03 0.1285133 at 100iterations 1.6646906E-03 5.2387238E-02 at 110iterations 7.5945753E-04 2.4701118E-02 at 120iterations finished qdiffx linear iterations at : 16:17:07 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 7.5945753E-04 2.4701118E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 16:17:08 9.027u 0.355s 0:10.19 91.9% 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 16:17:08 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 : 541.2822 centred at (gu) : 84.39013 79.91207 89.82340 assigned negative charge : -539.2841 centred at (gu) : 84.41540 79.65180 89.67429 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 202797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 grid for indexing accessible points = 1.400000 m= 99405 mr = 149896 m= 31764 mr = 81260 m= 6165 mr = 24936 m= 605 mr = 4494 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 1.810000 number of dielectric boundary points 79810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.960000 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 -0.3013082 -5.5779815E-02 midg,1,midg; midg,igrid,midg -0.2629246 5.8410194E-02 1,midg,midg; igrid,midg,midg 0.3669226 0.3909136 gauss-seidel spectral radius is 0.9992429 estimated iterations to convergence 287 setup time was (sec) 2.130000 now iterating at: 16:17:10 rms-change max change #iterations 10.77142 306.5807 at 10iterations 6.254350 159.2305 at 20iterations 3.606459 67.53437 at 30iterations 2.076913 42.71977 at 40iterations 1.192790 23.37304 at 50iterations 0.6835511 12.74198 at 60iterations 0.3919666 8.412012 at 70iterations 0.2245749 4.143890 at 80iterations 0.1284246 2.404621 at 90iterations 7.3471896E-02 1.304592 at 100iterations 4.1906465E-02 0.7418957 at 110iterations 2.3980608E-02 0.4246294 at 120iterations 1.3718342E-02 0.2498984 at 130iterations 7.8452500E-03 0.1549454 at 140iterations 4.4845063E-03 8.1576347E-02 at 150iterations 2.5608945E-03 4.1752815E-02 at 160iterations 1.4677993E-03 2.4333954E-02 at 170iterations 8.4416685E-04 1.4900208E-02 at 180iterations finished qdiffx linear iterations at : 16:17:24 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 8.4416685E-04 1.4900208E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 16:17:24 15.269u 0.471s 0:16.65 94.4% 0+0k 0+45400io 0pf+0w