___________________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 Nov 9 2009 at 14:24:42 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: 282 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 : 2.000013 assigned positive charge : 540.4482 centred at (gu) : 88.74218 87.75137 89.95990 assigned negative charge : -538.4501 centred at (gu) : 88.74824 87.69409 89.92862 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7880 nv = 96 ne = 84 npr = 75514 no. pairs analyzed = 75514 no. exposed pairs = 4085 no. arc points = 28552 no. surface atoms = 1382 nbur = 2156 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= 353 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 0.4200000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2978 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4399696E-10 1.9844408E-09 midg,1,midg; midg,igrid,midg -2.7669360E-09 1.8261577E-09 1,midg,midg; igrid,midg,midg 1.3077976E-09 3.7392989E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 14:24:43 rms-change max change #iterations 0.1192320 17.59689 at 10iterations 9.9574141E-03 1.444016 at 20iterations 8.3527894E-04 0.1197739 at 30iterations 7.2391231E-05 9.7999573E-03 at 40iterations 7.5126845E-06 1.0681152E-03 at 50iterations finished qdiffx linear iterations at : 14:24:46 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 7.5126845E-06 1.0681152E-03 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 14:24:47 3.928u 0.365s 0:05.12 83.5% 0+0k 1952+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 Mon Nov 9 2009 at 14:24:47 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 = 3538 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 : 3538 total number of charged atoms : 3390 net assigned charge : 2.000013 assigned positive charge : 540.4482 centred at (gu) : 86.22591 83.25326 89.87901 assigned negative charge : -538.4501 centred at (gu) : 86.24437 83.08183 89.78569 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 29515 mr = 61879 m= 3712 mr = 21454 m= 139 mr = 2125 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 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8300000 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 -2.2003761E-02 -5.1169549E-03 midg,1,midg; midg,igrid,midg -5.4125302E-03 1.1848673E-02 1,midg,midg; igrid,midg,midg 2.9443186E-02 2.9798932E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 14:24:48 rms-change max change #iterations 4.445515 152.0224 at 10iterations 2.020020 65.03342 at 20iterations 0.9132642 27.61996 at 30iterations 0.4166926 12.63042 at 40iterations 0.1886700 5.857425 at 50iterations 8.5789107E-02 2.493355 at 60iterations 3.8929816E-02 1.151543 at 70iterations 1.7689180E-02 0.6607952 at 80iterations 8.0401897E-03 0.2527733 at 90iterations 3.6572353E-03 0.1337204 at 100iterations 1.6631910E-03 5.3112030E-02 at 110iterations 7.5860147E-04 2.5131226E-02 at 120iterations finished qdiffx linear iterations at : 14:24:56 total time elapsed so far: 8.770000 # loops : 120 mean,max change (kT/e) : 7.5860147E-04 2.5131226E-02 energy calculations done at 8.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 14:24:57 8.948u 0.435s 0:10.18 92.0% 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 Nov 9 2009 at 14:24:57 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 = 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 : 2.000013 assigned positive charge : 540.4482 centred at (gu) : 84.33858 79.87954 89.81832 assigned negative charge : -538.4501 centred at (gu) : 84.36655 79.62259 89.67831 start vw surface at 0.1800000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 99417 mr = 149838 m= 31759 mr = 81234 m= 6154 mr = 24945 m= 604 mr = 4496 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 1.820000 number of dielectric boundary points 79877 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 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 -0.2905380 -5.8828678E-02 midg,1,midg; midg,igrid,midg -0.2630950 5.4601341E-02 1,midg,midg; igrid,midg,midg 0.3662429 0.3870631 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 14:24:59 rms-change max change #iterations 10.76194 306.6192 at 10iterations 6.249035 160.4539 at 20iterations 3.602980 70.49487 at 30iterations 2.076037 40.35772 at 40iterations 1.191776 23.36949 at 50iterations 0.6832873 14.31508 at 60iterations 0.3919577 7.485893 at 70iterations 0.2245789 3.853809 at 80iterations 0.1284114 2.123174 at 90iterations 7.3426947E-02 1.262909 at 100iterations 4.1919481E-02 0.7649555 at 110iterations 2.3992518E-02 0.4301593 at 120iterations 1.3718787E-02 0.2424922 at 130iterations 7.8516342E-03 0.1573486 at 140iterations 4.4892961E-03 7.9980850E-02 at 150iterations 2.5637888E-03 4.5322418E-02 at 160iterations 1.4701573E-03 2.4192810E-02 at 170iterations 8.4673968E-04 1.6584396E-02 at 180iterations finished qdiffx linear iterations at : 14:25:13 total time elapsed so far: 15.02000 # loops : 180 mean,max change (kT/e) : 8.4673968E-04 1.6584396E-02 energy calculations done at 15.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.19000 DelPhi exited at 14:25:13 15.194u 0.438s 0:16.49 94.7% 0+0k 0+45392io 0pf+0w