___________________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 May 13 2011 at 14:12:49 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: 285 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 : 541.5802 centred at (gu) : 88.75047 87.75690 89.95620 assigned negative charge : -539.5820 centred at (gu) : 88.75637 87.69963 89.92520 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 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 = 0.1900000 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= 353 mr = 4367 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 0.4100000 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 0.5200000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3545840E-10 1.9743904E-09 midg,1,midg; midg,igrid,midg -2.7710718E-09 1.8314626E-09 1,midg,midg; igrid,midg,midg 1.2978718E-09 3.7897288E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 14:12:50 rms-change max change #iterations 0.1194524 17.59689 at 10iterations 9.9817561E-03 1.452408 at 20iterations 8.3709852E-04 0.1198463 at 30iterations 7.2367140E-05 9.8094940E-03 at 40iterations 7.4064251E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 7.4064251E-06 1.0528564E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 14:12:54 3.895u 0.373s 0:04.66 91.4% 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 Fri May 13 2011 at 14:12:54 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: 285 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 : 541.5802 centred at (gu) : 86.25077 83.26984 89.86790 assigned negative charge : -539.5820 centred at (gu) : 86.26878 83.09845 89.77544 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 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 0.8400000 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 -2.1991858E-02 -5.1454543E-03 midg,1,midg; midg,igrid,midg -5.4616947E-03 1.1852330E-02 1,midg,midg; igrid,midg,midg 2.9419521E-02 2.9811883E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 14:12:55 rms-change max change #iterations 4.458008 152.0224 at 10iterations 2.026287 65.03340 at 20iterations 0.9161029 27.72532 at 30iterations 0.4180351 12.62975 at 40iterations 0.1892450 5.844643 at 50iterations 8.6047158E-02 2.522510 at 60iterations 3.9040986E-02 1.170261 at 70iterations 1.7745536E-02 0.6680546 at 80iterations 8.0650626E-03 0.2539291 at 90iterations 3.6677835E-03 0.1321850 at 100iterations 1.6681565E-03 5.2455902E-02 at 110iterations 7.6094276E-04 2.5316238E-02 at 120iterations finished qdiffx linear iterations at : 14:13:03 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 7.6094276E-04 2.5316238E-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 14:13:04 9.044u 0.380s 0:09.87 95.4% 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 Fri May 13 2011 at 14:13:04 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: 285 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 : 541.5802 centred at (gu) : 84.37587 79.90443 89.80166 assigned negative charge : -539.5820 centred at (gu) : 84.40315 79.64751 89.66290 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 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 = 1.080000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.800000 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 1.950000 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 -0.2904305 -5.9212845E-02 midg,1,midg; midg,igrid,midg -0.2636937 5.4556333E-02 1,midg,midg; igrid,midg,midg 0.3658734 0.3874610 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 14:13:06 rms-change max change #iterations 10.79975 306.6192 at 10iterations 6.271591 160.4542 at 20iterations 3.615557 71.55146 at 30iterations 2.083172 40.62543 at 40iterations 1.195814 23.05431 at 50iterations 0.6855649 14.47283 at 60iterations 0.3931969 7.606987 at 70iterations 0.2252961 3.854692 at 80iterations 0.1288093 2.140764 at 90iterations 7.3653422E-02 1.282784 at 100iterations 4.2045683E-02 0.7726440 at 110iterations 2.4065260E-02 0.4299173 at 120iterations 1.3760191E-02 0.2430239 at 130iterations 7.8753140E-03 0.1559753 at 140iterations 4.5024031E-03 8.0911636E-02 at 150iterations 2.5714096E-03 4.5482635E-02 at 160iterations 1.4741452E-03 2.4236679E-02 at 170iterations 8.4887230E-04 1.6407013E-02 at 180iterations finished qdiffx linear iterations at : 14:13:20 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 8.4887230E-04 1.6407013E-02 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 14:13:20 15.351u 0.472s 0:16.36 96.6% 0+0k 0+45392io 0pf+0w