------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/27/2006 at 13:10:57 [-O]verwriting output File Assignments: | MDIN: 1cgh-all-minimize.in | MDOUT: 1cgh--all-minimize.out |INPCRD: 1cgh-hold-protein.rst | PARM: 1cgh-water-box.top |RESTRT: 1cgh-all-minimize.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Entire system minimization &cntrl imin = 1, maxcyc = 1000, ncyc = 500, ntb = 1, ntr = 0, cut = 10 &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 31.092 | New format PARM file being parsed. | Version = 1.000 Date = 06/27/06 Time = 12:16:52 NATOM = 29776 NTYPES = 18 NBONH = 27929 MBONA = 1859 NTHETH = 4126 MTHETA = 2513 NPHIH = 7341 MPHIA = 3511 NHPARM = 0 NPARM = 0 NNB = 54902 NRES = 8953 NBONA = 1859 NTHETA = 2513 NPHIA = 3511 NUMBND = 46 NUMANG = 100 NPTRA = 38 NATYP = 31 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2392326 | Hollerith 187611 | Integer 1948727 | Max Pairs 17150976 | Max Rstack 1929334 | Max Istack 148880 | Total 109685 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 76.158 Box Y = 76.158 Box Z = 76.158 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 80 NFFT2 = 80 NFFT3 = 80 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 8698 Sum of charges from parm topology file = -0.00000025 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 9451764 | TOTAL SIZE OF NONBOND LIST = 9451764 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.1493E+05 1.3197E+00 4.9465E+01 C 20 BOND = 7689.8536 ANGLE = 537.5148 DIHED = 371.7255 VDWAALS = 16520.2259 EEL = -145753.1266 HBOND = 0.0000 1-4 VDW = 1023.7618 1-4 EEL = 4678.4368 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.1572E+05 1.0912E+00 2.5224E+01 C 20 BOND = 7742.7863 ANGLE = 555.4234 DIHED = 413.1948 VDWAALS = 16332.8895 EEL = -146034.6827 HBOND = 0.0000 1-4 VDW = 841.5380 1-4 EEL = 4432.5234 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.1600E+05 3.5392E-01 9.3913E+00 HG 102 BOND = 7755.7674 ANGLE = 571.0306 DIHED = 420.8331 VDWAALS = 16367.6583 EEL = -146283.8107 HBOND = 0.0000 1-4 VDW = 794.7931 1-4 EEL = 4373.8590 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.1621E+05 2.5224E-01 9.4246E+00 HG 102 BOND = 7783.4045 ANGLE = 580.1057 DIHED = 423.1942 VDWAALS = 16425.5357 EEL = -146531.3315 HBOND = 0.0000 1-4 VDW = 770.8682 1-4 EEL = 4341.0248 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.1638E+05 2.8719E-01 7.6161E+00 CZ 1140 BOND = 7809.4589 ANGLE = 585.8933 DIHED = 424.1694 VDWAALS = 16496.5940 EEL = -146773.0022 HBOND = 0.0000 1-4 VDW = 756.6463 1-4 EEL = 4320.0736 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.1653E+05 6.8222E-01 4.3961E+01 CE1 3307 BOND = 7839.1909 ANGLE = 590.1888 DIHED = 424.6626 VDWAALS = 16576.4489 EEL = -147014.2131 HBOND = 0.0000 1-4 VDW = 746.9376 1-4 EEL = 4305.5260 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.1668E+05 2.0334E-01 4.6268E+00 HG1 1939 BOND = 7855.5902 ANGLE = 592.6458 DIHED = 424.4725 VDWAALS = 16661.2801 EEL = -147251.6443 HBOND = 0.0000 1-4 VDW = 739.9390 1-4 EEL = 4294.5082 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -1.1682E+05 5.6276E-01 2.7944E+01 CE1 3307 BOND = 7881.8727 ANGLE = 595.3615 DIHED = 424.4161 VDWAALS = 16749.1196 EEL = -147487.1006 HBOND = 0.0000 1-4 VDW = 734.6728 1-4 EEL = 4285.7653 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.1694E+05 1.8720E-01 4.7179E+00 CE1 857 BOND = 7899.4365 ANGLE = 596.4530 DIHED = 424.5362 VDWAALS = 16832.4788 EEL = -147705.5193 HBOND = 0.0000 1-4 VDW = 730.6643 1-4 EEL = 4279.3186 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.1706E+05 5.1484E-01 3.8395E+01 CE1 857 BOND = 7922.2836 ANGLE = 598.5343 DIHED = 424.6321 VDWAALS = 16914.6118 EEL = -147917.4370 HBOND = 0.0000 1-4 VDW = 727.3355 1-4 EEL = 4274.1136 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.1717E+05 2.1909E-01 1.2487E+01 CE1 857 BOND = 7938.3124 ANGLE = 598.9052 DIHED = 424.5272 VDWAALS = 16993.0122 EEL = -148115.7830 HBOND = 0.0000 1-4 VDW = 724.5664 1-4 EEL = 4269.6867 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -1.1806E+05 6.0829E-01 3.9472E+01 N 837 BOND = 8177.4446 ANGLE = 620.2758 DIHED = 427.5082 VDWAALS = 17914.8969 EEL = -150135.2274 HBOND = 0.0000 1-4 VDW = 706.1075 1-4 EEL = 4225.6091 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.1830E+05 4.1164E-01 2.6431E+01 N 837 BOND = 8186.6607 ANGLE = 614.5485 DIHED = 423.0429 VDWAALS = 18008.8100 EEL = -150477.5264 HBOND = 0.0000 1-4 VDW = 707.4067 1-4 EEL = 4235.7072 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -1.1855E+05 3.4362E-01 1.9312E+01 N 837 BOND = 8223.1613 ANGLE = 612.9086 DIHED = 421.7512 VDWAALS = 18163.8076 EEL = -150912.5007 HBOND = 0.0000 1-4 VDW = 705.8463 1-4 EEL = 4234.1723 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.1882E+05 3.5662E-01 2.7882E+01 N 837 BOND = 8256.7763 ANGLE = 614.1244 DIHED = 420.4987 VDWAALS = 18341.2365 EEL = -151390.9655 HBOND = 0.0000 1-4 VDW = 705.3456 1-4 EEL = 4233.1216 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -1.1914E+05 4.3330E-01 2.9789E+01 N 837 BOND = 8316.5240 ANGLE = 613.9808 DIHED = 419.6643 VDWAALS = 18591.8289 EEL = -152015.4059 HBOND = 0.0000 1-4 VDW = 703.6975 1-4 EEL = 4232.3906 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -1.1926E+05 4.5327E-01 2.6682E+01 N 837 BOND = 8349.7220 ANGLE = 614.0053 DIHED = 419.3177 VDWAALS = 18675.3037 EEL = -152254.8353 HBOND = 0.0000 1-4 VDW = 703.1428 1-4 EEL = 4232.3866 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -1.1940E+05 3.9936E-01 2.8049E+01 N 837 BOND = 8350.2712 ANGLE = 614.3728 DIHED = 419.3154 VDWAALS = 18776.2921 EEL = -152498.2942 HBOND = 0.0000 1-4 VDW = 702.5150 1-4 EEL = 4232.1668 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.1954E+05 3.6835E-01 1.9757E+01 H 838 BOND = 8375.4752 ANGLE = 615.8849 DIHED = 419.2527 VDWAALS = 18874.9607 EEL = -152761.5871 HBOND = 0.0000 1-4 VDW = 701.8777 1-4 EEL = 4231.9034 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -1.1969E+05 3.1074E-01 1.3528E+01 CG2 998 BOND = 8397.9573 ANGLE = 615.4521 DIHED = 418.5228 VDWAALS = 18968.0209 EEL = -153020.1996 HBOND = 0.0000 1-4 VDW = 701.7565 1-4 EEL = 4232.8459 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.1995E+05 4.2193E-01 2.4550E+01 CD 1852 BOND = 8442.2255 ANGLE = 612.8353 DIHED = 417.4483 VDWAALS = 19165.3817 EEL = -153518.6753 HBOND = 0.0000 1-4 VDW = 700.6320 1-4 EEL = 4229.8849 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.1995E+05 4.2193E-01 2.4550E+01 CD 1852 BOND = 8442.2255 ANGLE = 612.8353 DIHED = 417.4483 VDWAALS = 19165.3817 EEL = -153518.6753 HBOND = 0.0000 1-4 VDW = 700.6320 1-4 EEL = 4229.8849 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.08 ( 0.01% of Total) | Build the list 10.41 (93.05% of List ) | Other 0.78 ( 6.95% of List ) | List time 11.19 ( 0.89% of Nonbo) | Short_ene time 1012.42 (99.27% of Direc) | Other 7.42 ( 0.73% of Direc) | Direct Ewald time 1019.84 (81.81% of Ewald) | Adjust Ewald time 6.34 ( 0.51% of Ewald) | Fill Bspline coeffs 8.07 ( 3.71% of Recip) | Fill charge grid 25.37 (11.66% of Recip) | Scalar sum 58.61 (26.94% of Recip) | Grad sum 34.31 (15.77% of Recip) | FFT time 91.20 (41.92% of Recip) | Recip Ewald time 217.57 (17.45% of Ewald) | Force Adjust 1.47 ( 0.12% of Ewald) | Virial junk 0.99 ( 0.08% of Ewald) | Start sycnronization 0.37 ( 0.03% of Ewald) | Ewald time 1246.60 (99.11% of Nonbo) | Nonbond force 1257.79 (99.19% of Force) | Bond/Angle/Dihedral 9.85 ( 0.78% of Force) | Other 0.46 ( 0.04% of Force) | Force time 1268.11 (100.0% of Runmd) | Runmd Time 1268.11 (98.96% of Total) | Other 13.19 ( 1.03% of Total) | Total time 1281.39 (100.0% of ALL ) | Highest rstack allocated: 1899802 | Highest istack allocated: 29776 | Job began at 13:10:57.128 on 06/27/2006 | Setup done at 13:10:57.925 on 06/27/2006 | Run done at 13:32:18.536 on 06/27/2006 | wallclock() was called 33024 times