__________DelPhi V. 4 Release 1.0_______________ | | | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | many dielectric regions, multisalt ionic | | strength, different probe radii, 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 | | Recompiled on Linux and PC | | January 2002 -------- Walter Rocchia | |__________________ ___________________| DelPhi V. 4 program started on Tue Jun 25 2002 at 19:33:33 opening parameter file delphi.prm.0.0 !!!!!!!!!!!!! the statement RADIOPT=1 could not be interpreted !!!!!!!!!!!!! !!!!!!!!!!!!! the statement PROC=1 could not be interpreted !!!!!!!!!!!!! atom radii read from file radios.siz # of radius parameter records: 4544 atomic charges read from file cargas.crg # of charge parameter records: 4544 assigning charges and radii... opening formatted file:fort.13 You are not reading from an objectfile! assuming having only molecules, and one dielectric medium number of atoms read in = 31 !!! WARNING: IN1 1 has a net charge of 0.0003 Direct mapping of epsilon: (0/1)(n/y) 1 time to read in and/or assign rad/chrg= 0.2471400 object number : 1, is a molecule pmid -0.3999999 -0.3500000 -0.2249999 grid size : 25 percent of box to be filled: 80.00000 scale,in grids/A : 2.000000 xmin,xmax (A): -4.241000 3.441000 ymin,ymax (A): -2.971000 2.271000 zmin,zmax (A): -5.241000 4.791000 x,y,z range (A): 7.682000 5.242000 10.03200 system geometric center in (A): -0.3999999 -0.3500000 -0.2249999 grid box is centered in (A) : -0.3999999 -0.3500000 -0.2249999 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 outer dielectric : 80.00000 dielectric in medium number 1 : 1.000000 first kind salt concentration (M) : 0.0000000E+00 valences salt 1 are 1 and 1 second kind salt concentration (M) : 0.0000000E+00 valences salt 2 are 0 and 0 ionic strength (M) : 0.0000000E+00 debye length (A) : 1000000. ion exclusion radius (A) : 2.000000 probe radius facing water(A: 1.600000 probe radius, internal (A) : 1.600000 boundary conditions : coulombic x,y,z periodic bc. flags : F F F # of linear iterations : 500 # of non-linear iterations : 0 non-linear energy calculat.: F manual relaxation parameter : F ionic direct energy contribution: F concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : F map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off start vw surface at 0.2479260 Starting creating Vand der Waals Epsilon Map Ending creating Vand der Waals Epsilon Map fill in re-entrant regions at 0.2490840 boundary points facing water= 0 total number of boundary points before elab.= 0 radpmax,radprb 1.600000 1.600000 1.600000 # of vertices = 384 # of edges = 372 # of pairs = 127 time to find all pairs = 4.4700000E-04 # pairs analyzed (atom-atom and atom-object)= 127 # exposed pairs (atom-atom and atom-object)= 94 no. arc points = 5555 no. surface atoms = 31 nbur = 0 mkacc time = 2.6950000E-03 writing accessible surface arcs data to ARCDAT grid for indexing accessible points = 1.600000 bgp added m= 0 bgp removed mr = 0 time to grow re-entrant surface = 9.7300002E-04 no. cavity mid-points inaccessible to solvent = 0 after surface elaboration ibnum= 0 and ibnumsurf= 0 scaling boundary grid points % of boundary points contacting solvent = nan time taken = 3.3570000E-03 0 points had to be assigned by global comparison time to turn everything in is 0.2625400 number of charges coming from molecules 31 number of charge distrib. present 0 number of atom coordinates read : 31 total number of assigned charges : 31 net assigned charge : 2.9993057E-04 assigned positive charge : 4.713001 centred at (gu) : 15.15984 12.22544 16.73340 assigned negative charge : -4.712700 centred at (gu) : 15.21472 12.60526 16.78852 number of dielectric boundary points 0 no. dielectric boundary points in salt = 0 no. grid points charged and not internal= 232 ## out of them, 232 charged points are in solution ## iepsmp to db, and charging done at 0.2681060 number of grid points assigned charge 232 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 0.2545883 -0.2316480 midg,1,midg; midg,igrid,midg 7.7854641E-02 -0.3151846 1,midg,midg; igrid,midg,midg 3.1729661E-02 2.1349959E-02 gauss-seidel spectral radius is 0.9829621315 estimated iterations to convergence 63 setup time was (sec) 0.2880880 now iterating at: 19:33:34 rms-change max change #iterations 32.18156 0.4237407 at 10 iterations 0.1723479 2.7910814E-02 at 20 iterations 8.7842625E-04 2.1034032E-03 at 30 iterations 5.0054414E-06 1.3512373E-04 at 40 iterations 2.6433435E-08 9.7933225E-06 at 50 iterations 2.4376662E-10 1.9073486E-06 at 60 iterations 9.7576683E-11 1.9073486E-06 at 70 iterations 8.9407939E-11 1.9073486E-06 at 80 iterations 8.9927371E-11 1.9073486E-06 at 90 iterations 8.9005942E-11 1.9073486E-06 at 100 iterations 9.1245268E-11 1.9073486E-06 at 110 iterations 8.8027197E-11 1.9073486E-06 at 120 iterations 8.6632160E-11 1.9073486E-06 at 130 iterations 8.3770046E-11 1.9073486E-06 at 140 iterations 9.7996292E-11 1.9073486E-06 at 150 iterations 1.0203930E-10 2.8610229E-06 at 160 iterations 9.7533343E-11 1.9073486E-06 at 170 iterations 8.5136842E-11 1.9073486E-06 at 180 iterations 9.4341160E-11 1.9073486E-06 at 190 iterations 7.7082729E-11 1.9073486E-06 at 200 iterations 1.0731414E-10 3.8146973E-06 at 210 iterations 8.7107349E-11 1.9073486E-06 at 220 iterations 9.1385594E-11 1.6689301E-06 at 230 iterations 8.3567951E-11 1.9073486E-06 at 240 iterations 7.9673962E-11 1.9073486E-06 at 250 iterations 1.0078756E-10 1.9073486E-06 at 260 iterations 1.0565653E-10 2.8610229E-06 at 270 iterations 9.8802161E-11 1.9073486E-06 at 280 iterations 7.9813031E-11 1.9073486E-06 at 290 iterations 9.0381036E-11 1.9073486E-06 at 300 iterations 1.0018968E-10 1.9073486E-06 at 310 iterations 1.0086956E-10 1.9073486E-06 at 320 iterations 9.3374780E-11 1.9073486E-06 at 330 iterations 8.3995103E-11 1.9073486E-06 at 340 iterations 8.3123758E-11 1.9073486E-06 at 350 iterations 9.1735106E-11 1.9073486E-06 at 360 iterations 8.5762036E-11 1.9073486E-06 at 370 iterations 9.7298419E-11 3.3378601E-06 at 380 iterations 8.0867549E-11 1.9073486E-06 at 390 iterations 8.9121224E-11 1.9073486E-06 at 400 iterations 9.0631183E-11 2.8610229E-06 at 410 iterations 8.0870338E-11 1.9073486E-06 at 420 iterations 9.6445837E-11 2.3841858E-06 at 430 iterations 1.0503434E-10 2.3841858E-06 at 440 iterations 9.6033209E-11 1.9073486E-06 at 450 iterations 9.5146904E-11 1.9073486E-06 at 460 iterations 9.6669894E-11 1.9073486E-06 at 470 iterations 8.9720550E-11 1.1920929E-06 at 480 iterations 8.6992746E-11 1.9073486E-06 at 490 iterations 8.0026229E-11 1.9073486E-06 at 500 iterations finished qdiffx linear iterations at : 19:33:34 total time elapsed so far: 0.4158970 # loops : 500 mean,max change (kT/e) : 8.0026229E-11 1.9073486E-06 total grid energy : 43.87386 kt self-reaction field energy : 0.0000000E+00 kt total s.charge,no epsin carrying : 0.0000 corrected reaction field energy: 0.0000000E+00 kt total reaction field energy : 0.0000000E+00 kt All energy terms but grid and self_react.: 0.0000000E+00kt energy calculations done at 0.4161490 total cpu time was (sec) 0.4161580 DelPhi exited at 19:33:34