------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/24/2004 at 16:32:39 [-O]verwriting output File Assignments: | MDIN: polyAT_wat_min1.in | MDOUT: polyAT_wat_min1.out |INPCRD: polyAT_wat.inpcrd | PARM: polyAT_wat.prmtop |RESTRT: restrt | REFC: polyAT_wat.inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: polyA-polyT 10-mer: initial minimisation solvent + ions &cntrl imin = 1, maxcyc = 1000, ncyc = 500, ntb = 1, ntr = 1, cut = 10 &end Hold the DNA fixed 500.0 RES 1 20 END 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 = 21.666 | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 17:07:52 NATOM = 9560 NTYPES = 17 NBONH = 9138 MBONA = 452 NTHETH = 554 MTHETA = 694 NPHIH = 1077 MPHIA = 1238 NHPARM = 0 NPARM = 0 NNB = 15434 NRES = 3006 NBONA = 452 NTHETA = 694 NPHIA = 1238 NUMBND = 34 NUMANG = 59 NPTRA = 39 NATYP = 27 NPHB = 1 IFBOX = 2 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 863235 | Hollerith 60368 | Integer 593444 | Max Pairs 5506560 | Max Rstack 615500 | Max Istack 47800 | Total 35803 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 = 1 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 = 53.071 Box Y = 53.071 Box Z = 53.071 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 54 NFFT2 = 54 NFFT3 = 54 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the DNA fixed GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000 GRP 1 RES 1 TO 20 Number of atoms in this group = 638 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 2968 Sum of charges from parm topology file = 0.00000008 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 = 2868248 | TOTAL SIZE OF NONBOND LIST = 2868248 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.4745E+04 3.6907E+01 2.6855E+03 O 9021 BOND = 929.5040 ANGLE = 544.5351 DIHED = 456.0253 VDWAALS = 4213.0014 EEL = -30872.1933 HBOND = 0.0000 1-4 VDW = 264.8124 1-4 EEL = -280.3135 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.1706E+04 4.7703E+00 2.5530E+02 O5' 2 BOND = 1805.1807 ANGLE = 433.8532 DIHED = 452.6629 VDWAALS = 2886.9246 EEL = -37647.8151 HBOND = 0.0000 1-4 VDW = 247.2084 1-4 EEL = -296.1433 RESTRAINT = 412.5073 EAMBER = -32118.1286 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.3249E+04 2.7267E+00 1.5343E+02 O5' 2 BOND = 1973.1538 ANGLE = 430.9537 DIHED = 452.6025 VDWAALS = 3110.3075 EEL = -39408.8649 HBOND = 0.0000 1-4 VDW = 247.9842 1-4 EEL = -295.0312 RESTRAINT = 239.5446 EAMBER = -33488.8945 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -3.4047E+04 1.1859E+00 3.4614E+01 C5 239 BOND = 1985.2190 ANGLE = 433.9779 DIHED = 452.6266 VDWAALS = 3354.5885 EEL = -40517.2876 HBOND = 0.0000 1-4 VDW = 247.9235 1-4 EEL = -295.2818 RESTRAINT = 291.2772 EAMBER = -34338.2338 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -3.4525E+04 2.9414E+00 1.3785E+02 C5 239 BOND = 2064.7457 ANGLE = 439.2131 DIHED = 452.6089 VDWAALS = 3581.0796 EEL = -41310.5408 HBOND = 0.0000 1-4 VDW = 247.5695 1-4 EEL = -295.7940 RESTRAINT = 295.6312 EAMBER = -34821.1178 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -3.4925E+04 1.7356E+00 7.3458E+01 C5 239 BOND = 2109.6404 ANGLE = 435.0510 DIHED = 452.6717 VDWAALS = 3781.4099 EEL = -41948.7515 HBOND = 0.0000 1-4 VDW = 249.0843 1-4 EEL = -294.3040 RESTRAINT = 290.6157 EAMBER = -35215.1981 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -3.5229E+04 2.5212E+00 8.8903E+01 C5 239 BOND = 2164.4649 ANGLE = 437.8233 DIHED = 452.7409 VDWAALS = 3966.7371 EEL = -42499.0283 HBOND = 0.0000 1-4 VDW = 249.2721 1-4 EEL = -293.7690 RESTRAINT = 292.3644 EAMBER = -35521.7590 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -3.5515E+04 1.4650E+00 4.6401E+01 C6 272 BOND = 2201.0338 ANGLE = 433.9120 DIHED = 452.6390 VDWAALS = 4141.5534 EEL = -42987.9019 HBOND = 0.0000 1-4 VDW = 248.1295 1-4 EEL = -295.6484 RESTRAINT = 291.1986 EAMBER = -35806.2825 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -3.5744E+04 2.1369E+00 6.4719E+01 C6 272 BOND = 2244.6500 ANGLE = 434.7729 DIHED = 452.6153 VDWAALS = 4304.2824 EEL = -43425.2926 HBOND = 0.0000 1-4 VDW = 248.0959 1-4 EEL = -296.1182 RESTRAINT = 293.4771 EAMBER = -36036.9943 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -3.5960E+04 1.2317E+00 6.1987E+01 C2 245 BOND = 2273.0092 ANGLE = 435.1734 DIHED = 452.7442 VDWAALS = 4453.3080 EEL = -43818.6568 HBOND = 0.0000 1-4 VDW = 248.4522 1-4 EEL = -294.1113 RESTRAINT = 289.8087 EAMBER = -36250.0809 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -3.6142E+04 1.7179E+00 9.8849E+01 C2 245 BOND = 2308.3590 ANGLE = 435.5868 DIHED = 452.7195 VDWAALS = 4594.9986 EEL = -44179.0511 HBOND = 0.0000 1-4 VDW = 248.3960 1-4 EEL = -294.0026 RESTRAINT = 291.0365 EAMBER = -36432.9937 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -3.7153E+04 1.3761E+00 5.0451E+01 H1 2872 BOND = 2515.9548 ANGLE = 436.2250 DIHED = 452.9495 VDWAALS = 5536.0029 EEL = -46338.8383 HBOND = 0.0000 1-4 VDW = 248.2741 1-4 EEL = -294.9482 RESTRAINT = 291.6150 EAMBER = -37444.3801 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -3.7554E+04 1.1107E+00 3.7810E+01 Na+ 652 BOND = 2578.5218 ANGLE = 434.7012 DIHED = 452.9774 VDWAALS = 5806.6889 EEL = -47069.4442 HBOND = 0.0000 1-4 VDW = 248.1148 1-4 EEL = -294.6934 RESTRAINT = 289.5750 EAMBER = -37843.1335 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -3.7879E+04 1.1875E+00 7.9656E+01 Na+ 652 BOND = 2641.9082 ANGLE = 435.1722 DIHED = 453.0621 VDWAALS = 6081.3107 EEL = -47733.7773 HBOND = 0.0000 1-4 VDW = 248.1980 1-4 EEL = -295.0014 RESTRAINT = 289.7485 EAMBER = -38169.1275 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -3.8122E+04 1.0954E+00 9.0082E+01 Na+ 652 BOND = 2670.7354 ANGLE = 434.8998 DIHED = 452.9312 VDWAALS = 6280.4142 EEL = -48202.6742 HBOND = 0.0000 1-4 VDW = 248.0744 1-4 EEL = -294.9518 RESTRAINT = 288.9096 EAMBER = -38410.5710 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -3.8350E+04 1.5273E+00 7.9470E+01 P 446 BOND = 2734.8621 ANGLE = 434.7952 DIHED = 452.7846 VDWAALS = 6509.7113 EEL = -48724.3049 HBOND = 0.0000 1-4 VDW = 248.2425 1-4 EEL = -295.1426 RESTRAINT = 289.1807 EAMBER = -38639.0518 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -3.8544E+04 8.7407E-01 2.5146E+01 O2P 33 BOND = 2769.4145 ANGLE = 435.0518 DIHED = 452.7084 VDWAALS = 6609.0349 EEL = -49051.7045 HBOND = 0.0000 1-4 VDW = 248.1285 1-4 EEL = -295.2484 RESTRAINT = 288.4090 EAMBER = -38832.6149 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -3.8667E+04 7.5582E-01 3.0504E+01 P 446 BOND = 2790.5449 ANGLE = 434.4086 DIHED = 452.7688 VDWAALS = 6665.2761 EEL = -49251.9602 HBOND = 0.0000 1-4 VDW = 248.4155 1-4 EEL = -294.9503 RESTRAINT = 288.1757 EAMBER = -38955.4965 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -3.8795E+04 7.7763E-01 2.9659E+01 Na+ 651 BOND = 2808.4000 ANGLE = 433.8664 DIHED = 452.8242 VDWAALS = 6762.0673 EEL = -49494.5055 HBOND = 0.0000 1-4 VDW = 248.3155 1-4 EEL = -294.7799 RESTRAINT = 289.0759 EAMBER = -39083.8119 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -3.8897E+04 5.4768E-01 2.9570E+01 P 446 BOND = 2819.5789 ANGLE = 433.6979 DIHED = 452.8365 VDWAALS = 6822.3999 EEL = -49665.6200 HBOND = 0.0000 1-4 VDW = 248.3152 1-4 EEL = -294.7238 RESTRAINT = 286.7833 EAMBER = -39183.5154 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -3.8989E+04 5.9208E-01 2.7355E+01 P 446 BOND = 2829.9826 ANGLE = 433.7389 DIHED = 452.8278 VDWAALS = 6893.6489 EEL = -49839.8168 HBOND = 0.0000 1-4 VDW = 248.3104 1-4 EEL = -294.6786 RESTRAINT = 286.5245 EAMBER = -39275.9867 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -3.8989E+04 5.9208E-01 2.7355E+01 P 446 BOND = 2829.9826 ANGLE = 433.7389 DIHED = 452.8278 VDWAALS = 6893.6489 EEL = -49839.8168 HBOND = 0.0000 1-4 VDW = 248.3104 1-4 EEL = -294.6786 RESTRAINT = 286.5245 EAMBER = -39275.9867 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.02 ( 0.01% of Total) | Build the list 3.50 (91.76% of List ) | Other 0.31 ( 8.24% of List ) | List time 3.82 ( 1.11% of Nonbo) | Short_ene time 272.71 (99.24% of Direc) | Other 2.08 ( 0.76% of Direc) | Direct Ewald time 274.78 (80.76% of Ewald) | Adjust Ewald time 1.55 ( 0.45% of Ewald) | Fill Bspline coeffs 2.35 ( 3.71% of Recip) | Fill charge grid 7.66 (12.11% of Recip) | Scalar sum 16.80 (26.55% of Recip) | Grad sum 9.92 (15.67% of Recip) | FFT time 26.54 (41.95% of Recip) | Other 0.01 ( 0.01% of Recip) | Recip Ewald time 63.27 (18.60% of Ewald) | Force Adjust 0.25 ( 0.07% of Ewald) | Virial junk 0.28 ( 0.08% of Ewald) | Start sycnronization 0.09 ( 0.03% of Ewald) | Ewald time 340.23 (98.89% of Nonbo) | Nonbond force 344.05 (99.39% of Force) | Bond/Angle/Dihedral 1.99 ( 0.57% of Force) | Other 0.11 ( 0.03% of Force) | Force time 346.15 (100.0% of Runmd) | Runmd Time 346.15 (99.54% of Total) | Other 1.59 ( 0.46% of Total) | Total time 347.76 (100.0% of ALL ) | Highest rstack allocated: 606106 | Highest istack allocated: 9560 | Job began at 16:32:39.377 on 02/24/2004 | Setup done at 16:32:39.565 on 02/24/2004 | Run done at 16:38:27.142 on 02/24/2004 | wallclock() was called 33026 times