------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/27/2006 at 14:44:49 [-O]verwriting output File Assignments: | MDIN: 1cgh-md-restr.in | MDOUT: 1cgh-md-restr.out |INPCRD: 1cgh-all-minimize.rst | PARM: 1cgh-water-box.top |RESTRT: 1cgh-md-restr.rst | REFC: 1cgh-all-minimize.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: 1cgh: 1ps MD with restraints on protein &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 5000, dt = 0.002 ntpr = 100, ntwx = 100, ntwr = 1000 / Keep protein fixed with weak restraints 10.0 RES 1 228 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 = 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 2154088 | Hollerith 187611 | Integer 1948727 | Max Pairs 17150976 | Max Rstack 1929334 | Max Istack 148880 | Total 107824 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, 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 Molecular dynamics: nstlim = 5000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 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 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Keep protein fixed with weak restraints GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000 GRP 1 RES 1 TO 228 Number of atoms in this group = 3655 ----- 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: 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 = 9463132 | TOTAL SIZE OF NONBOND LIST = 9463132 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -128258.4911 EKtot = 0.0000 EPtot = -128258.4911 BOND = 134.0022 ANGLE = 612.8353 DIHED = 417.4483 1-4 NB = 700.6320 1-4 EEL = 4229.8849 VDWAALS = 19165.3817 EELEC = -153518.6755 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1079E-03 ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 63.25 PRESS = 0.0 Etot = -105117.9023 EKtot = 3858.3975 EPtot = -108976.2998 BOND = 237.9451 ANGLE = 821.1682 DIHED = 470.4906 1-4 NB = 709.8515 1-4 EEL = 4232.9481 VDWAALS = 13877.3218 EELEC = -129452.1561 EHBOND = 0.0000 RESTRAINT = 126.1311 EAMBER (non-restraint) = -109102.4309 Ewald error estimate: 0.1303E-03 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 108.90 PRESS = 0.0 Etot = -100005.3264 EKtot = 6643.1196 EPtot = -106648.4460 BOND = 312.4742 ANGLE = 1001.2716 DIHED = 501.0750 1-4 NB = 728.7344 1-4 EEL = 4222.6129 VDWAALS = 14087.9031 EELEC = -127718.0337 EHBOND = 0.0000 RESTRAINT = 215.5165 EAMBER (non-restraint) = -106863.9625 Ewald error estimate: 0.1883E-04 ------------------------------------------------------------------------------ NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = 142.74 PRESS = 0.0 Etot = -95838.9266 EKtot = 8707.8268 EPtot = -104546.7534 BOND = 366.9790 ANGLE = 1157.0049 DIHED = 537.9567 1-4 NB = 742.9766 1-4 EEL = 4222.1986 VDWAALS = 13758.3271 EELEC = -125641.4026 EHBOND = 0.0000 RESTRAINT = 309.2064 EAMBER (non-restraint) = -104855.9598 Ewald error estimate: 0.4953E-04 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 171.19 PRESS = 0.0 Etot = -92479.4390 EKtot = 10443.2700 EPtot = -102922.7090 BOND = 443.0391 ANGLE = 1259.1711 DIHED = 558.1640 1-4 NB = 735.3763 1-4 EEL = 4166.2007 VDWAALS = 13400.1381 EELEC = -123860.1962 EHBOND = 0.0000 RESTRAINT = 375.3978 EAMBER (non-restraint) = -103298.1068 Ewald error estimate: 0.5933E-04 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 194.36 PRESS = 0.0 Etot = -89555.0737 EKtot = 11856.7108 EPtot = -101411.7845 BOND = 476.5227 ANGLE = 1360.1839 DIHED = 599.2297 1-4 NB = 747.1642 1-4 EEL = 4230.1386 VDWAALS = 12857.9704 EELEC = -122119.9012 EHBOND = 0.0000 RESTRAINT = 436.9073 EAMBER (non-restraint) = -101848.6918 Ewald error estimate: 0.1223E-03 ------------------------------------------------------------------------------ NSTEP = 600 TIME(PS) = 1.200 TEMP(K) = 210.34 PRESS = 0.0 Etot = -87140.0405 EKtot = 12831.2141 EPtot = -99971.2546 BOND = 520.4890 ANGLE = 1435.3678 DIHED = 592.1920 1-4 NB = 753.3927 1-4 EEL = 4195.4345 VDWAALS = 12674.1250 EELEC = -120611.1267 EHBOND = 0.0000 RESTRAINT = 468.8710 EAMBER (non-restraint) = -100440.1256 Ewald error estimate: 0.7377E-04 ------------------------------------------------------------------------------ NSTEP = 700 TIME(PS) = 1.400 TEMP(K) = 225.89 PRESS = 0.0 Etot = -85080.7014 EKtot = 13779.8446 EPtot = -98860.5460 BOND = 536.9926 ANGLE = 1498.8255 DIHED = 614.8859 1-4 NB = 769.3178 1-4 EEL = 4178.4619 VDWAALS = 12568.6474 EELEC = -119530.8721 EHBOND = 0.0000 RESTRAINT = 503.1951 EAMBER (non-restraint) = -99363.7411 Ewald error estimate: 0.1573E-03 ------------------------------------------------------------------------------ NSTEP = 800 TIME(PS) = 1.600 TEMP(K) = 238.93 PRESS = 0.0 Etot = -83401.9078 EKtot = 14575.2248 EPtot = -97977.1326 BOND = 561.2732 ANGLE = 1492.1070 DIHED = 635.9766 1-4 NB = 764.4864 1-4 EEL = 4218.2729 VDWAALS = 11996.4169 EELEC = -118165.8710 EHBOND = 0.0000 RESTRAINT = 520.2055 EAMBER (non-restraint) = -98497.3380 Ewald error estimate: 0.2311E-04 ------------------------------------------------------------------------------ NSTEP = 900 TIME(PS) = 1.800 TEMP(K) = 247.00 PRESS = 0.0 Etot = -82086.1467 EKtot = 15067.5403 EPtot = -97153.6870 BOND = 542.3140 ANGLE = 1609.1833 DIHED = 632.8274 1-4 NB = 762.0246 1-4 EEL = 4232.9266 VDWAALS = 11760.2657 EELEC = -117258.1108 EHBOND = 0.0000 RESTRAINT = 564.8822 EAMBER (non-restraint) = -97718.5692 Ewald error estimate: 0.2715E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.003643 0.02(Removed) NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 255.56 PRESS = 0.0 Etot = -80781.4696 EKtot = 15589.6226 EPtot = -96371.0922 BOND = 607.6656 ANGLE = 1638.3194 DIHED = 634.1090 1-4 NB = 765.4845 1-4 EEL = 4196.8870 VDWAALS = 11466.0854 EELEC = -116269.1975 EHBOND = 0.0000 RESTRAINT = 589.5543 EAMBER (non-restraint) = -96960.6466 Ewald error estimate: 0.5653E-04 ------------------------------------------------------------------------------ NSTEP = 1100 TIME(PS) = 2.200 TEMP(K) = 261.25 PRESS = 0.0 Etot = -79774.5038 EKtot = 15936.7402 EPtot = -95711.2440 BOND = 626.2170 ANGLE = 1672.7193 DIHED = 658.4087 1-4 NB = 778.2931 1-4 EEL = 4226.0718 VDWAALS = 11203.2323 EELEC = -115475.6597 EHBOND = 0.0000 RESTRAINT = 599.4735 EAMBER (non-restraint) = -96310.7175 Ewald error estimate: 0.5142E-04 ------------------------------------------------------------------------------ NSTEP = 1200 TIME(PS) = 2.400 TEMP(K) = 264.26 PRESS = 0.0 Etot = -78927.7050 EKtot = 16120.6556 EPtot = -95048.3606 BOND = 624.2642 ANGLE = 1672.6837 DIHED = 646.7253 1-4 NB = 775.2710 1-4 EEL = 4228.8420 VDWAALS = 11097.4949 EELEC = -114709.4861 EHBOND = 0.0000 RESTRAINT = 615.8442 EAMBER (non-restraint) = -95664.2048 Ewald error estimate: 0.7923E-04 ------------------------------------------------------------------------------ NSTEP = 1300 TIME(PS) = 2.600 TEMP(K) = 270.99 PRESS = 0.0 Etot = -78121.2864 EKtot = 16531.3383 EPtot = -94652.6247 BOND = 591.3545 ANGLE = 1688.0973 DIHED = 662.5705 1-4 NB = 785.9579 1-4 EEL = 4227.1056 VDWAALS = 10772.7878 EELEC = -113990.8907 EHBOND = 0.0000 RESTRAINT = 610.3925 EAMBER (non-restraint) = -95263.0171 Ewald error estimate: 0.2634E-04 ------------------------------------------------------------------------------ NSTEP = 1400 TIME(PS) = 2.800 TEMP(K) = 273.12 PRESS = 0.0 Etot = -77523.7303 EKtot = 16661.3569 EPtot = -94185.0872 BOND = 647.9232 ANGLE = 1713.0634 DIHED = 652.3008 1-4 NB = 782.2973 1-4 EEL = 4223.5292 VDWAALS = 10865.4740 EELEC = -113713.5367 EHBOND = 0.0000 RESTRAINT = 643.8616 EAMBER (non-restraint) = -94828.9488 Ewald error estimate: 0.8706E-04 ------------------------------------------------------------------------------ NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 276.94 PRESS = 0.0 Etot = -76927.7382 EKtot = 16893.9955 EPtot = -93821.7337 BOND = 653.6943 ANGLE = 1753.4430 DIHED = 664.0645 1-4 NB = 774.2994 1-4 EEL = 4191.6912 VDWAALS = 10429.6025 EELEC = -112926.2243 EHBOND = 0.0000 RESTRAINT = 637.6956 EAMBER (non-restraint) = -94459.4293 Ewald error estimate: 0.1155E-04 ------------------------------------------------------------------------------ NSTEP = 1600 TIME(PS) = 3.200 TEMP(K) = 281.07 PRESS = 0.0 Etot = -76490.1631 EKtot = 17145.8380 EPtot = -93636.0011 BOND = 649.9682 ANGLE = 1694.6818 DIHED = 686.9464 1-4 NB = 787.3170 1-4 EEL = 4202.8711 VDWAALS = 10529.7449 EELEC = -112831.2387 EHBOND = 0.0000 RESTRAINT = 643.7082 EAMBER (non-restraint) = -94279.7093 Ewald error estimate: 0.1806E-03 ------------------------------------------------------------------------------ NSTEP = 1700 TIME(PS) = 3.400 TEMP(K) = 282.54 PRESS = 0.0 Etot = -75981.4039 EKtot = 17235.7726 EPtot = -93217.1765 BOND = 678.1604 ANGLE = 1700.3303 DIHED = 672.0921 1-4 NB = 771.4883 1-4 EEL = 4197.9534 VDWAALS = 10586.9011 EELEC = -112472.2248 EHBOND = 0.0000 RESTRAINT = 648.1227 EAMBER (non-restraint) = -93865.2991 Ewald error estimate: 0.1833E-03 ------------------------------------------------------------------------------ NSTEP = 1800 TIME(PS) = 3.600 TEMP(K) = 284.27 PRESS = 0.0 Etot = -75652.0596 EKtot = 17341.0082 EPtot = -92993.0678 BOND = 645.5375 ANGLE = 1716.7191 DIHED = 690.2904 1-4 NB = 780.5508 1-4 EEL = 4177.2264 VDWAALS = 10342.3294 EELEC = -112002.4590 EHBOND = 0.0000 RESTRAINT = 656.7376 EAMBER (non-restraint) = -93649.8054 Ewald error estimate: 0.4127E-04 ------------------------------------------------------------------------------ NSTEP = 1900 TIME(PS) = 3.800 TEMP(K) = 285.25 PRESS = 0.0 Etot = -75181.1285 EKtot = 17400.7748 EPtot = -92581.9034 BOND = 613.8516 ANGLE = 1766.7677 DIHED = 663.8721 1-4 NB = 779.6258 1-4 EEL = 4228.5121 VDWAALS = 10501.6898 EELEC = -111804.3768 EHBOND = 0.0000 RESTRAINT = 668.1543 EAMBER (non-restraint) = -93250.0576 Ewald error estimate: 0.9286E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.003328 0.02(Removed) NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 286.52 PRESS = 0.0 Etot = -74968.3886 EKtot = 17478.7143 EPtot = -92447.1028 BOND = 649.6248 ANGLE = 1774.3309 DIHED = 665.7410 1-4 NB = 789.9573 1-4 EEL = 4179.7729 VDWAALS = 9953.3055 EELEC = -111120.2377 EHBOND = 0.0000 RESTRAINT = 660.4025 EAMBER (non-restraint) = -93107.5053 Ewald error estimate: 0.1209E-03 ------------------------------------------------------------------------------ NSTEP = 2100 TIME(PS) = 4.200 TEMP(K) = 289.17 PRESS = 0.0 Etot = -74794.2676 EKtot = 17639.9951 EPtot = -92434.2627 BOND = 631.7453 ANGLE = 1759.7964 DIHED = 674.7448 1-4 NB = 774.4278 1-4 EEL = 4194.7649 VDWAALS = 10173.8478 EELEC = -111334.7210 EHBOND = 0.0000 RESTRAINT = 691.1313 EAMBER (non-restraint) = -93125.3940 Ewald error estimate: 0.3469E-04 ------------------------------------------------------------------------------ NSTEP = 2200 TIME(PS) = 4.400 TEMP(K) = 291.14 PRESS = 0.0 Etot = -74522.2751 EKtot = 17760.3318 EPtot = -92282.6069 BOND = 653.7168 ANGLE = 1757.2717 DIHED = 672.2871 1-4 NB = 787.0273 1-4 EEL = 4185.6625 VDWAALS = 9856.4375 EELEC = -110884.1796 EHBOND = 0.0000 RESTRAINT = 689.1697 EAMBER (non-restraint) = -92971.7767 Ewald error estimate: 0.2089E-04 ------------------------------------------------------------------------------ NSTEP = 2300 TIME(PS) = 4.600 TEMP(K) = 290.92 PRESS = 0.0 Etot = -74226.1654 EKtot = 17747.0715 EPtot = -91973.2369 BOND = 683.2582 ANGLE = 1792.8043 DIHED = 664.9023 1-4 NB = 780.9816 1-4 EEL = 4176.3960 VDWAALS = 9983.6183 EELEC = -110733.8970 EHBOND = 0.0000 RESTRAINT = 678.6995 EAMBER (non-restraint) = -92651.9363 Ewald error estimate: 0.5615E-04 ------------------------------------------------------------------------------ NSTEP = 2400 TIME(PS) = 4.800 TEMP(K) = 289.61 PRESS = 0.0 Etot = -74145.6348 EKtot = 17667.1817 EPtot = -91812.8165 BOND = 649.6064 ANGLE = 1784.1099 DIHED = 667.0502 1-4 NB = 786.1304 1-4 EEL = 4202.4105 VDWAALS = 9839.1992 EELEC = -110431.3337 EHBOND = 0.0000 RESTRAINT = 690.0105 EAMBER (non-restraint) = -92502.8270 Ewald error estimate: 0.1266E-03 ------------------------------------------------------------------------------ NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 294.67 PRESS = 0.0 Etot = -73949.8845 EKtot = 17975.3938 EPtot = -91925.2783 BOND = 650.6269 ANGLE = 1804.0141 DIHED = 654.6750 1-4 NB = 779.7643 1-4 EEL = 4193.5174 VDWAALS = 10165.0950 EELEC = -110841.0152 EHBOND = 0.0000 RESTRAINT = 668.0442 EAMBER (non-restraint) = -92593.3225 Ewald error estimate: 0.2073E-03 ------------------------------------------------------------------------------ NSTEP = 2600 TIME(PS) = 5.200 TEMP(K) = 292.50 PRESS = 0.0 Etot = -73787.1308 EKtot = 17843.3897 EPtot = -91630.5205 BOND = 691.3795 ANGLE = 1769.2573 DIHED = 649.5949 1-4 NB = 782.7458 1-4 EEL = 4233.1645 VDWAALS = 9499.9012 EELEC = -109932.4006 EHBOND = 0.0000 RESTRAINT = 675.8368 EAMBER (non-restraint) = -92306.3574 Ewald error estimate: 0.1524E-04 ------------------------------------------------------------------------------ NSTEP = 2700 TIME(PS) = 5.400 TEMP(K) = 295.87 PRESS = 0.0 Etot = -73585.6644 EKtot = 18049.1159 EPtot = -91634.7803 BOND = 694.1357 ANGLE = 1754.2586 DIHED = 676.0105 1-4 NB = 778.7826 1-4 EEL = 4200.0227 VDWAALS = 9866.0034 EELEC = -110263.3292 EHBOND = 0.0000 RESTRAINT = 659.3354 EAMBER (non-restraint) = -92294.1157 Ewald error estimate: 0.5275E-04 ------------------------------------------------------------------------------ NSTEP = 2800 TIME(PS) = 5.600 TEMP(K) = 295.55 PRESS = 0.0 Etot = -73532.1902 EKtot = 18029.6454 EPtot = -91561.8356 BOND = 663.2931 ANGLE = 1763.3263 DIHED = 678.8926 1-4 NB = 790.3243 1-4 EEL = 4194.5517 VDWAALS = 9705.1205 EELEC = -110016.9718 EHBOND = 0.0000 RESTRAINT = 659.6278 EAMBER (non-restraint) = -92221.4634 Ewald error estimate: 0.3717E-04 ------------------------------------------------------------------------------ NSTEP = 2900 TIME(PS) = 5.800 TEMP(K) = 293.24 PRESS = 0.0 Etot = -73488.4671 EKtot = 17888.3042 EPtot = -91376.7714 BOND = 686.2305 ANGLE = 1766.0421 DIHED = 646.4028 1-4 NB = 781.3499 1-4 EEL = 4226.6673 VDWAALS = 9659.5988 EELEC = -109805.1110 EHBOND = 0.0000 RESTRAINT = 662.0483 EAMBER (non-restraint) = -92038.8196 Ewald error estimate: 0.8403E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.002081 0.01(Removed) NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 294.84 PRESS = 0.0 Etot = -73332.3282 EKtot = 17985.8326 EPtot = -91318.1608 BOND = 636.3562 ANGLE = 1742.3009 DIHED = 654.1856 1-4 NB = 778.2832 1-4 EEL = 4245.7504 VDWAALS = 9556.7366 EELEC = -109591.5668 EHBOND = 0.0000 RESTRAINT = 659.7931 EAMBER (non-restraint) = -91977.9539 Ewald error estimate: 0.1518E-04 ------------------------------------------------------------------------------ NSTEP = 3100 TIME(PS) = 6.200 TEMP(K) = 296.10 PRESS = 0.0 Etot = -73158.4182 EKtot = 18062.9183 EPtot = -91221.3365 BOND = 649.0163 ANGLE = 1780.0960 DIHED = 663.8344 1-4 NB = 782.7758 1-4 EEL = 4227.6572 VDWAALS = 9386.3429 EELEC = -109389.7162 EHBOND = 0.0000 RESTRAINT = 678.6570 EAMBER (non-restraint) = -91899.9935 Ewald error estimate: 0.1239E-03 ------------------------------------------------------------------------------ NSTEP = 3200 TIME(PS) = 6.400 TEMP(K) = 298.93 PRESS = 0.0 Etot = -73074.7690 EKtot = 18235.6017 EPtot = -91310.3706 BOND = 667.5492 ANGLE = 1744.3747 DIHED = 650.7988 1-4 NB = 791.1702 1-4 EEL = 4211.7763 VDWAALS = 9280.0303 EELEC = -109336.5114 EHBOND = 0.0000 RESTRAINT = 680.4414 EAMBER (non-restraint) = -91990.8120 Ewald error estimate: 0.1102E-03 ------------------------------------------------------------------------------ NSTEP = 3300 TIME(PS) = 6.600 TEMP(K) = 297.88 PRESS = 0.0 Etot = -73066.0749 EKtot = 18171.6001 EPtot = -91237.6749 BOND = 645.8659 ANGLE = 1804.4944 DIHED = 682.6636 1-4 NB = 790.2571 1-4 EEL = 4177.9084 VDWAALS = 9488.6983 EELEC = -109496.2317 EHBOND = 0.0000 RESTRAINT = 668.6690 EAMBER (non-restraint) = -91906.3439 Ewald error estimate: 0.1394E-03 ------------------------------------------------------------------------------ NSTEP = 3400 TIME(PS) = 6.800 TEMP(K) = 300.05 PRESS = 0.0 Etot = -72833.8524 EKtot = 18304.1858 EPtot = -91138.0382 BOND = 694.0347 ANGLE = 1772.0003 DIHED = 664.0973 1-4 NB = 793.6298 1-4 EEL = 4235.8429 VDWAALS = 9469.7573 EELEC = -109423.1623 EHBOND = 0.0000 RESTRAINT = 655.7618 EAMBER (non-restraint) = -91793.8000 Ewald error estimate: 0.6618E-04 ------------------------------------------------------------------------------ NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 297.92 PRESS = 0.0 Etot = -72764.5031 EKtot = 18173.9302 EPtot = -90938.4333 BOND = 667.7610 ANGLE = 1808.3209 DIHED = 676.2404 1-4 NB = 778.0653 1-4 EEL = 4175.7816 VDWAALS = 9274.1422 EELEC = -108971.7515 EHBOND = 0.0000 RESTRAINT = 653.0068 EAMBER (non-restraint) = -91591.4401 Ewald error estimate: 0.1351E-05 ------------------------------------------------------------------------------ NSTEP = 3600 TIME(PS) = 7.200 TEMP(K) = 297.79 PRESS = 0.0 Etot = -72697.9888 EKtot = 18166.0267 EPtot = -90864.0155 BOND = 672.8233 ANGLE = 1772.6663 DIHED = 686.5675 1-4 NB = 785.6292 1-4 EEL = 4245.3404 VDWAALS = 9534.3340 EELEC = -109222.3397 EHBOND = 0.0000 RESTRAINT = 660.9635 EAMBER (non-restraint) = -91524.9790 Ewald error estimate: 0.6456E-04 ------------------------------------------------------------------------------ NSTEP = 3700 TIME(PS) = 7.400 TEMP(K) = 298.52 PRESS = 0.0 Etot = -72572.1674 EKtot = 18210.8205 EPtot = -90782.9878 BOND = 643.1963 ANGLE = 1822.8062 DIHED = 694.1729 1-4 NB = 775.0577 1-4 EEL = 4216.2653 VDWAALS = 9560.2884 EELEC = -109161.8358 EHBOND = 0.0000 RESTRAINT = 667.0611 EAMBER (non-restraint) = -91450.0490 Ewald error estimate: 0.1656E-03 ------------------------------------------------------------------------------ NSTEP = 3800 TIME(PS) = 7.600 TEMP(K) = 302.48 PRESS = 0.0 Etot = -72416.6190 EKtot = 18451.9212 EPtot = -90868.5401 BOND = 703.1481 ANGLE = 1777.9916 DIHED = 671.4122 1-4 NB = 776.9316 1-4 EEL = 4172.9110 VDWAALS = 9252.1914 EELEC = -108906.4810 EHBOND = 0.0000 RESTRAINT = 683.3550 EAMBER (non-restraint) = -91551.8951 Ewald error estimate: 0.1183E-03 ------------------------------------------------------------------------------ NSTEP = 3900 TIME(PS) = 7.800 TEMP(K) = 301.34 PRESS = 0.0 Etot = -72502.8446 EKtot = 18382.8553 EPtot = -90885.6998 BOND = 647.5087 ANGLE = 1770.2007 DIHED = 656.4274 1-4 NB = 777.4222 1-4 EEL = 4275.5194 VDWAALS = 9239.6288 EELEC = -108944.0788 EHBOND = 0.0000 RESTRAINT = 691.6719 EAMBER (non-restraint) = -91577.3717 Ewald error estimate: 0.2141E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.001734 0.00(Removed) NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 297.88 PRESS = 0.0 Etot = -72684.0497 EKtot = 18171.8055 EPtot = -90855.8552 BOND = 688.8692 ANGLE = 1785.1080 DIHED = 673.5620 1-4 NB = 768.0243 1-4 EEL = 4254.1539 VDWAALS = 9383.5483 EELEC = -109095.8714 EHBOND = 0.0000 RESTRAINT = 686.7506 EAMBER (non-restraint) = -91542.6058 Ewald error estimate: 0.9535E-04 ------------------------------------------------------------------------------ NSTEP = 4100 TIME(PS) = 8.200 TEMP(K) = 300.81 PRESS = 0.0 Etot = -72588.2990 EKtot = 18350.5057 EPtot = -90938.8047 BOND = 637.3997 ANGLE = 1830.1583 DIHED = 666.3399 1-4 NB = 775.7011 1-4 EEL = 4201.8823 VDWAALS = 9556.6449 EELEC = -109282.7738 EHBOND = 0.0000 RESTRAINT = 675.8429 EAMBER (non-restraint) = -91614.6476 Ewald error estimate: 0.1337E-03 ------------------------------------------------------------------------------ NSTEP = 4200 TIME(PS) = 8.400 TEMP(K) = 302.04 PRESS = 0.0 Etot = -72411.1433 EKtot = 18425.2194 EPtot = -90836.3626 BOND = 672.9519 ANGLE = 1800.9881 DIHED = 666.2594 1-4 NB = 775.8742 1-4 EEL = 4250.7979 VDWAALS = 9469.3733 EELEC = -109139.9164 EHBOND = 0.0000 RESTRAINT = 667.3090 EAMBER (non-restraint) = -91503.6716 Ewald error estimate: 0.6865E-04 ------------------------------------------------------------------------------ NSTEP = 4300 TIME(PS) = 8.600 TEMP(K) = 302.65 PRESS = 0.0 Etot = -72318.6131 EKtot = 18462.5500 EPtot = -90781.1630 BOND = 672.4248 ANGLE = 1780.5444 DIHED = 667.7351 1-4 NB = 767.9810 1-4 EEL = 4233.1179 VDWAALS = 9298.3709 EELEC = -108868.7855 EHBOND = 0.0000 RESTRAINT = 667.4484 EAMBER (non-restraint) = -91448.6114 Ewald error estimate: 0.7247E-04 ------------------------------------------------------------------------------ NSTEP = 4400 TIME(PS) = 8.800 TEMP(K) = 300.08 PRESS = 0.0 Etot = -72430.2853 EKtot = 18305.9732 EPtot = -90736.2585 BOND = 682.9079 ANGLE = 1775.9272 DIHED = 647.6824 1-4 NB = 772.6224 1-4 EEL = 4243.2391 VDWAALS = 9453.4592 EELEC = -108980.4549 EHBOND = 0.0000 RESTRAINT = 668.3581 EAMBER (non-restraint) = -91404.6167 Ewald error estimate: 0.6553E-05 ------------------------------------------------------------------------------ NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 297.99 PRESS = 0.0 Etot = -72556.4842 EKtot = 18178.1330 EPtot = -90734.6173 BOND = 687.1099 ANGLE = 1765.5311 DIHED = 666.2893 1-4 NB = 790.7522 1-4 EEL = 4236.0562 VDWAALS = 9443.6031 EELEC = -109016.7476 EHBOND = 0.0000 RESTRAINT = 692.7885 EAMBER (non-restraint) = -91427.4058 Ewald error estimate: 0.8978E-05 ------------------------------------------------------------------------------ NSTEP = 4600 TIME(PS) = 9.200 TEMP(K) = 301.04 PRESS = 0.0 Etot = -72632.8041 EKtot = 18364.1683 EPtot = -90996.9724 BOND = 671.2496 ANGLE = 1743.3112 DIHED = 643.7522 1-4 NB = 797.3533 1-4 EEL = 4227.6450 VDWAALS = 9368.8927 EELEC = -109122.3945 EHBOND = 0.0000 RESTRAINT = 673.2179 EAMBER (non-restraint) = -91670.1903 Ewald error estimate: 0.1154E-03 ------------------------------------------------------------------------------ NSTEP = 4700 TIME(PS) = 9.400 TEMP(K) = 302.35 PRESS = 0.0 Etot = -72614.1084 EKtot = 18443.9056 EPtot = -91058.0140 BOND = 631.7532 ANGLE = 1765.7099 DIHED = 645.3663 1-4 NB = 778.1430 1-4 EEL = 4204.4596 VDWAALS = 9381.1884 EELEC = -109126.1101 EHBOND = 0.0000 RESTRAINT = 661.4758 EAMBER (non-restraint) = -91719.4898 Ewald error estimate: 0.5852E-04 ------------------------------------------------------------------------------ NSTEP = 4800 TIME(PS) = 9.600 TEMP(K) = 299.90 PRESS = 0.0 Etot = -72462.8431 EKtot = 18294.7728 EPtot = -90757.6158 BOND = 666.5081 ANGLE = 1807.8628 DIHED = 654.8460 1-4 NB = 780.7113 1-4 EEL = 4196.1367 VDWAALS = 9423.0788 EELEC = -108953.1632 EHBOND = 0.0000 RESTRAINT = 666.4037 EAMBER (non-restraint) = -91424.0196 Ewald error estimate: 0.1602E-03 ------------------------------------------------------------------------------ NSTEP = 4900 TIME(PS) = 9.800 TEMP(K) = 300.51 PRESS = 0.0 Etot = -72503.9102 EKtot = 18332.0785 EPtot = -90835.9888 BOND = 653.4086 ANGLE = 1797.5259 DIHED = 668.7027 1-4 NB = 776.5321 1-4 EEL = 4213.8012 VDWAALS = 9242.1101 EELEC = -108848.3564 EHBOND = 0.0000 RESTRAINT = 660.2871 EAMBER (non-restraint) = -91496.2759 Ewald error estimate: 0.2511E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.003842 0.02(Removed) NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 300.22 PRESS = 0.0 Etot = -72494.1768 EKtot = 18314.5485 EPtot = -90808.7253 BOND = 703.6928 ANGLE = 1807.8390 DIHED = 677.5886 1-4 NB = 785.2180 1-4 EEL = 4189.9058 VDWAALS = 9516.7123 EELEC = -109147.2030 EHBOND = 0.0000 RESTRAINT = 657.5210 EAMBER (non-restraint) = -91466.2464 Ewald error estimate: 0.7590E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 5000 S T E P S NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 268.07 PRESS = 0.0 Etot = -77641.1105 EKtot = 16353.3271 EPtot = -93994.4376 BOND = 617.7996 ANGLE = 1667.5914 DIHED = 643.7859 1-4 NB = 770.4710 1-4 EEL = 4207.6967 VDWAALS = 10493.4621 EELEC = -113000.0187 EHBOND = 0.0000 RESTRAINT = 604.7743 EAMBER (non-restraint) = -94599.2119 Ewald error estimate: 0.6694E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 56.91 PRESS = 0.0 Etot = 8185.1121 EKtot = 3471.6119 EPtot = 4745.1956 BOND = 107.7070 ANGLE = 234.9096 DIHED = 50.1280 1-4 NB = 17.5513 1-4 EEL = 22.8204 VDWAALS = 1538.5613 EELEC = 5739.3192 EHBOND = 0.0000 RESTRAINT = 134.0201 EAMBER (non-restraint) = 4611.1755 Ewald error estimate: 0.4885E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Build the list 663.68 (99.36% of List ) | Other 4.26 ( 0.64% of List ) | List time 667.94 ( 9.66% of Nonbo) | Short_ene time 5056.78 (99.26% of Direc) | Other 37.60 ( 0.74% of Direc) | Direct Ewald time 5094.39 (81.59% of Ewald) | Adjust Ewald time 31.60 ( 0.51% of Ewald) | Fill Bspline coeffs 40.65 ( 3.68% of Recip) | Fill charge grid 132.36 (12.00% of Recip) | Scalar sum 292.08 (26.47% of Recip) | Grad sum 171.39 (15.53% of Recip) | FFT time 466.91 (42.31% of Recip) | Recip Ewald time 1103.43 (17.67% of Ewald) | Force Adjust 7.54 ( 0.12% of Ewald) | Virial junk 4.90 ( 0.08% of Ewald) | Start sycnronization 1.87 ( 0.03% of Ewald) | Ewald time 6243.84 (90.34% of Nonbo) | Nonbond force 6911.79 (99.39% of Force) | Bond/Angle/Dihedral 39.59 ( 0.57% of Force) | Other 2.75 ( 0.04% of Force) | Force time 6954.13 (96.80% of Runmd) | Shake time 32.84 ( 0.46% of Runmd) | Verlet update time 196.62 ( 2.74% of Runmd) | Runmd Time 7183.68 (100.0% of Total) | Other 0.69 ( 0.01% of Total) | Total time 7184.46 (100.0% of ALL ) | Highest rstack allocated: 1899802 | Highest istack allocated: 29776 | Job began at 14:44:49.066 on 06/27/2006 | Setup done at 14:44:49.849 on 06/27/2006 | Run done at 16:44:33.530 on 06/27/2006 | wallclock() was called 196065 times