___________________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 15:10:08 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: 290 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 : 541.7802 centred at (gu) : 88.75325 87.75758 89.95749 assigned negative charge : -539.7820 centred at (gu) : 88.75926 87.70034 89.92630 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 0.4100000 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 -5.4379973E-10 1.9829660E-09 midg,1,midg; midg,igrid,midg -2.7706584E-09 1.8315968E-09 1,midg,midg; igrid,midg,midg 1.3028226E-09 3.7580999E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 15:10:09 rms-change max change #iterations 0.1194738 17.59689 at 10iterations 9.9844495E-03 1.452839 at 20iterations 8.3714514E-04 0.1198797 at 30iterations 7.2375187E-05 9.8285675E-03 at 40iterations 7.4114228E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 15:10:12 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 7.4114228E-06 1.0528564E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 15:10:13 3.917u 0.357s 0:04.87 87.4% 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 15:10:13 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 = 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 : 2.000013 assigned positive charge : 541.7802 centred at (gu) : 86.25912 83.27193 89.87176 assigned negative charge : -539.7820 centred at (gu) : 86.27744 83.10059 89.77874 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 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 0.7200000 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 0.8600000 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 -2.2001194E-02 -5.0932784E-03 midg,1,midg; midg,igrid,midg -5.4619000E-03 1.1848247E-02 1,midg,midg; igrid,midg,midg 2.9420389E-02 2.9751563E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 15:10:14 rms-change max change #iterations 4.459782 152.0224 at 10iterations 2.026937 65.03339 at 20iterations 0.9164708 27.75534 at 30iterations 0.4181904 12.61777 at 40iterations 0.1893146 5.849313 at 50iterations 8.6076677E-02 2.519889 at 60iterations 3.9052073E-02 1.174238 at 70iterations 1.7751338E-02 0.6721935 at 80iterations 8.0679320E-03 0.2543449 at 90iterations 3.6688356E-03 0.1322994 at 100iterations 1.6687802E-03 5.2234650E-02 at 110iterations 7.6123513E-04 2.5444984E-02 at 120iterations finished qdiffx linear iterations at : 15:10:23 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 7.6123513E-04 2.5444984E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 15:10:23 9.097u 0.400s 0:10.27 92.4% 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 15:10:23 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 = 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: 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 : 541.7802 centred at (gu) : 84.38840 79.90755 89.80745 assigned negative charge : -539.7820 centred at (gu) : 84.41615 79.65073 89.66786 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 = 1.090000 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 -0.2905314 -5.8541939E-02 midg,1,midg; midg,igrid,midg -0.2637216 5.4515447E-02 1,midg,midg; igrid,midg,midg 0.3658830 0.3861770 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 15:10:26 rms-change max change #iterations 10.80274 306.6193 at 10iterations 6.273303 160.8196 at 20iterations 3.616460 71.90976 at 30iterations 2.083730 40.62544 at 40iterations 1.196148 22.90825 at 50iterations 0.6857532 14.45667 at 60iterations 0.3933001 7.607777 at 70iterations 0.2253493 3.861692 at 80iterations 0.1288405 2.148731 at 90iterations 7.3669590E-02 1.282143 at 100iterations 4.2056847E-02 0.7703991 at 110iterations 2.4070954E-02 0.4298720 at 120iterations 1.3763385E-02 0.2430115 at 130iterations 7.8772325E-03 0.1561508 at 140iterations 4.5034857E-03 8.1111908E-02 at 150iterations 2.5720587E-03 4.5574188E-02 at 160iterations 1.4745008E-03 2.4248123E-02 at 170iterations 8.4907067E-04 1.6374588E-02 at 180iterations finished qdiffx linear iterations at : 15:10:40 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 8.4907067E-04 1.6374588E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 15:10:41 15.952u 0.427s 0:17.25 94.8% 0+0k 0+45392io 0pf+0w