------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 12/10/2009 at 15:00:20 [-O]verwriting output File Assignments: | MDIN: min6.in | MDOUT: min6.out |INPCRD: prmcrd | PARM: prmtop |RESTRT: min6.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization Step 6 &cntrl igb = 0, imin = 1, ntx = 1, irest = 0, ntb = 2, maxcyc = 1000, ncyc = 500, drms = 0.0001, ntpr = 25, ntwx = 100, iwrap = 1, cut = 8.0, dielc = 1.0, ntc = 1, ntf = 1, ntt = 3, tempi = 300.0, temp0 = 300.0, gamma_ln=5.0, tautp = 0.5, ig = 71277, vlimit = 10.0, ntp = 1, taup = 1.0, ntr = 0, ibelly = 0, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 12.085 | New format PARM file being parsed. | Version = 1.000 Date = 12/10/09 Time = 14:59:49 NATOM = 642 NTYPES = 10 NBONH = 246 MBONA = 278 NTHETH = 611 MTHETA = 178 NPHIH = 15 MPHIA = 102 NHPARM = 0 NPARM = 0 NNB = 1520 NRES = 122 NBONA = 278 NTHETA = 178 NPHIA = 102 NUMBND = 19 NUMANG = 30 NPTRA = 10 NATYP = 13 NPHB = 0 IFBOX = 1 NMXRS = 37 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 122565 | Hollerith 3976 | Integer 41667 | Max Pairs 205761 | nblistReal 7704 | nblist Int 64326 | Total 2251 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- LIG 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 = 25, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, 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 = 0 Box X = 30.422 Box Y = 27.367 Box Z = 24.170 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 30 NFFT2 = 27 NFFT3 = 24 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- LIG begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00012099 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 = 43432 | TOTAL SIZE OF NONBOND LIST = 43432 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.2074E+03 9.7376E+00 8.3053E+01 C3 16 BOND = 89.3347 ANGLE = 38.9034 DIHED = 52.3834 VDWAALS = -436.0849 EEL = 403.8122 HBOND = 0.0000 1-4 VDW = 22.1269 1-4 EEL = -1377.8467 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 25 -1.3564E+03 2.6354E+00 4.0739E+01 C13 21 BOND = 7.8118 ANGLE = 16.0514 DIHED = 52.4457 VDWAALS = -438.2842 EEL = 408.0495 HBOND = 0.0000 1-4 VDW = 30.3760 1-4 EEL = -1432.8941 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.3638E+03 3.4994E-01 7.5300E+00 O4 6 BOND = 7.6215 ANGLE = 21.1100 DIHED = 50.6499 VDWAALS = -438.4044 EEL = 411.4729 HBOND = 0.0000 1-4 VDW = 31.9397 1-4 EEL = -1448.2226 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 75 -1.3677E+03 4.0752E-01 7.9489E+00 O4 6 BOND = 8.5365 ANGLE = 23.8764 DIHED = 47.0716 VDWAALS = -437.9102 EEL = 413.1402 HBOND = 0.0000 1-4 VDW = 32.5468 1-4 EEL = -1454.9293 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.3715E+03 5.8639E-01 9.7366E+00 C13 21 BOND = 8.9627 ANGLE = 25.6307 DIHED = 42.4203 VDWAALS = -437.0529 EEL = 413.6985 HBOND = 0.0000 1-4 VDW = 32.8560 1-4 EEL = -1457.9763 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 125 -1.3747E+03 7.7540E-01 1.2934E+01 C13 21 BOND = 9.2105 ANGLE = 27.1401 DIHED = 37.9861 VDWAALS = -436.2029 EEL = 413.7636 HBOND = 0.0000 1-4 VDW = 33.0161 1-4 EEL = -1459.6144 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.3771E+03 9.2017E-01 1.5175E+01 C13 21 BOND = 9.4365 ANGLE = 28.4184 DIHED = 34.5028 VDWAALS = -435.5986 EEL = 413.6532 HBOND = 0.0000 1-4 VDW = 33.0920 1-4 EEL = -1460.6308 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 175 -1.3793E+03 4.4807E-01 5.5135E+00 C13 21 BOND = 9.7535 ANGLE = 29.2368 DIHED = 31.7980 VDWAALS = -435.2408 EEL = 413.5289 HBOND = 0.0000 1-4 VDW = 33.1531 1-4 EEL = -1461.5197 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.3807E+03 5.9861E-01 7.8280E+00 C7 27 BOND = 9.9538 ANGLE = 30.0980 DIHED = 29.8987 VDWAALS = -435.0543 EEL = 413.3571 HBOND = 0.0000 1-4 VDW = 33.1980 1-4 EEL = -1462.1148 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 225 -1.3817E+03 6.5979E-01 9.4509E+00 C3 16 BOND = 10.1538 ANGLE = 30.6786 DIHED = 28.6257 VDWAALS = -434.9894 EEL = 413.1841 HBOND = 0.0000 1-4 VDW = 33.2041 1-4 EEL = -1462.5419 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.3827E+03 1.9203E-01 1.8547E+00 C7 27 BOND = 9.9250 ANGLE = 31.3150 DIHED = 27.7472 VDWAALS = -435.0030 EEL = 412.9741 HBOND = 0.0000 1-4 VDW = 33.2213 1-4 EEL = -1462.8421 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 275 -1.3833E+03 3.8270E-01 4.6366E+00 C7 27 BOND = 9.9703 ANGLE = 31.7127 DIHED = 27.1393 VDWAALS = -435.0662 EEL = 412.7585 HBOND = 0.0000 1-4 VDW = 33.2346 1-4 EEL = -1463.0913 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.3840E+03 1.3718E-01 1.3733E+00 O4 6 BOND = 10.0479 ANGLE = 31.9047 DIHED = 26.7056 VDWAALS = -435.1682 EEL = 412.5325 HBOND = 0.0000 1-4 VDW = 33.2533 1-4 EEL = -1463.3022 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 325 -1.3846E+03 1.3627E-01 1.1269E+00 O4 6 BOND = 10.0824 ANGLE = 32.0821 DIHED = 26.4047 VDWAALS = -435.2845 EEL = 412.2906 HBOND = 0.0000 1-4 VDW = 33.2619 1-4 EEL = -1463.4425 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -1.3852E+03 1.9300E-01 2.2641E+00 C3 16 BOND = 10.1466 ANGLE = 32.1847 DIHED = 26.1761 VDWAALS = -435.4313 EEL = 412.0265 HBOND = 0.0000 1-4 VDW = 33.2627 1-4 EEL = -1463.5479 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 375 -1.3857E+03 3.5667E-01 4.8474E+00 C3 16 BOND = 10.2277 ANGLE = 32.2470 DIHED = 26.0062 VDWAALS = -435.5856 EEL = 411.7499 HBOND = 0.0000 1-4 VDW = 33.2665 1-4 EEL = -1463.6285 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.3863E+03 4.1386E-01 6.1478E+00 C3 16 BOND = 10.3241 ANGLE = 32.2494 DIHED = 25.8791 VDWAALS = -435.7540 EEL = 411.4635 HBOND = 0.0000 1-4 VDW = 33.2450 1-4 EEL = -1463.6731 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 425 -1.3869E+03 1.5053E-01 1.1438E+00 C3 16 BOND = 10.1164 ANGLE = 32.4639 DIHED = 25.7863 VDWAALS = -435.9210 EEL = 411.1516 HBOND = 0.0000 1-4 VDW = 33.2862 1-4 EEL = -1463.7423 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.3874E+03 1.2595E-01 1.0685E+00 I1 24 BOND = 10.1325 ANGLE = 32.4909 DIHED = 25.7092 VDWAALS = -436.0996 EEL = 410.8349 HBOND = 0.0000 1-4 VDW = 33.2889 1-4 EEL = -1463.7816 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 475 -1.3880E+03 2.2183E-01 2.5598E+00 C19 2 BOND = 10.1329 ANGLE = 32.5408 DIHED = 25.6463 VDWAALS = -436.2885 EEL = 410.4867 HBOND = 0.0000 1-4 VDW = 33.2920 1-4 EEL = -1463.8200 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.3886E+03 3.3546E-01 4.4819E+00 C19 2 BOND = 10.1478 ANGLE = 32.5779 DIHED = 25.5983 VDWAALS = -436.4651 EEL = 410.1408 HBOND = 0.0000 1-4 VDW = 33.2942 1-4 EEL = -1463.8543 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 525 -1.4095E+03 3.8406E-01 3.9933E+00 C1 189 BOND = 10.7215 ANGLE = 32.2987 DIHED = 26.5357 VDWAALS = -441.7357 EEL = 394.4994 HBOND = 0.0000 1-4 VDW = 34.0885 1-4 EEL = -1465.9191 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -1.4167E+03 9.4397E-01 1.2896E+01 C5 23 BOND = 9.9924 ANGLE = 32.5529 DIHED = 29.3719 VDWAALS = -444.5581 EEL = 386.6101 HBOND = 0.0000 1-4 VDW = 32.9363 1-4 EEL = -1463.5822 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 575 -1.4220E+03 6.0232E-01 7.5894E+00 C18 3 BOND = 10.8022 ANGLE = 34.6570 DIHED = 25.6544 VDWAALS = -445.0463 EEL = 385.2040 HBOND = 0.0000 1-4 VDW = 33.4491 1-4 EEL = -1466.7617 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.4261E+03 7.3790E-01 8.8366E+00 C20 5 BOND = 9.5496 ANGLE = 33.7796 DIHED = 25.2398 VDWAALS = -445.0404 EEL = 380.1388 HBOND = 0.0000 1-4 VDW = 33.2445 1-4 EEL = -1463.0606 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 625 -1.4298E+03 6.2859E-01 8.7594E+00 C18 3 BOND = 10.8281 ANGLE = 34.5031 DIHED = 24.9141 VDWAALS = -445.9330 EEL = 378.8975 HBOND = 0.0000 1-4 VDW = 33.3286 1-4 EEL = -1466.3510 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -1.4343E+03 8.3296E-01 9.2706E+00 C16 4 BOND = 9.5173 ANGLE = 34.0463 DIHED = 25.3492 VDWAALS = -446.0669 EEL = 372.7127 HBOND = 0.0000 1-4 VDW = 32.9201 1-4 EEL = -1462.7763 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 675 -1.4383E+03 5.1122E-01 6.8799E+00 C18 3 BOND = 10.6217 ANGLE = 34.0524 DIHED = 24.8700 VDWAALS = -446.8769 EEL = 371.8837 HBOND = 0.0000 1-4 VDW = 33.0475 1-4 EEL = -1465.9073 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.4427E+03 1.1344E+00 1.0883E+01 C6 15 BOND = 10.2392 ANGLE = 34.6614 DIHED = 25.0721 VDWAALS = -447.1111 EEL = 365.0695 HBOND = 0.0000 1-4 VDW = 32.9073 1-4 EEL = -1463.4992 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 725 -1.4471E+03 4.8964E-01 5.7103E+00 C7 27 BOND = 10.7406 ANGLE = 33.9288 DIHED = 24.7177 VDWAALS = -447.8733 EEL = 364.3056 HBOND = 0.0000 1-4 VDW = 33.0202 1-4 EEL = -1465.9606 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -1.4564E+03 1.3504E+00 1.6228E+01 H2 276 BOND = 12.0555 ANGLE = 36.0791 DIHED = 24.9247 VDWAALS = -448.4418 EEL = 349.2985 HBOND = 0.0000 1-4 VDW = 31.4086 1-4 EEL = -1461.6989 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 775 -1.4623E+03 2.7263E-01 3.1974E+00 Cl3 1 BOND = 10.8292 ANGLE = 34.2431 DIHED = 24.5140 VDWAALS = -448.9953 EEL = 350.7389 HBOND = 0.0000 1-4 VDW = 33.0153 1-4 EEL = -1466.6327 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -1.4729E+03 1.9259E+00 1.8811E+01 C17 10 BOND = 12.3521 ANGLE = 39.8606 DIHED = 25.8048 VDWAALS = -449.6248 EEL = 332.1760 HBOND = 0.0000 1-4 VDW = 31.4979 1-4 EEL = -1464.9233 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 825 -1.4810E+03 3.0641E-01 3.5150E+00 C3 16 BOND = 10.7446 ANGLE = 35.2216 DIHED = 24.6693 VDWAALS = -450.7351 EEL = 334.1579 HBOND = 0.0000 1-4 VDW = 33.1607 1-4 EEL = -1468.2085 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -1.4889E+03 1.3131E+00 1.4812E+01 C14 14 BOND = 12.3975 ANGLE = 35.2543 DIHED = 24.6586 VDWAALS = -452.4896 EEL = 324.3164 HBOND = 0.0000 1-4 VDW = 31.9962 1-4 EEL = -1465.0423 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 875 -1.4941E+03 3.2055E-01 3.6535E+00 C9 29 BOND = 10.8580 ANGLE = 34.5809 DIHED = 24.6975 VDWAALS = -453.3217 EEL = 323.3802 HBOND = 0.0000 1-4 VDW = 32.9730 1-4 EEL = -1467.3069 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.4993E+03 9.5036E-01 1.1671E+01 C14 14 BOND = 11.1775 ANGLE = 37.2824 DIHED = 25.5953 VDWAALS = -454.3832 EEL = 316.2994 HBOND = 0.0000 1-4 VDW = 31.8180 1-4 EEL = -1467.0844 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 925 -1.5027E+03 3.7749E-01 4.6356E+00 C2 17 BOND = 10.9932 ANGLE = 36.4142 DIHED = 25.1782 VDWAALS = -455.0906 EEL = 316.6161 HBOND = 0.0000 1-4 VDW = 33.0759 1-4 EEL = -1469.8585 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -1.5066E+03 8.5358E-01 8.8304E+00 C15 12 BOND = 11.3838 ANGLE = 35.0487 DIHED = 24.9687 VDWAALS = -455.5804 EEL = 312.1936 HBOND = 0.0000 1-4 VDW = 32.5680 1-4 EEL = -1467.1414 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 975 -1.5089E+03 3.7377E-01 3.6006E+00 Cl4 9 BOND = 11.1456 ANGLE = 35.7170 DIHED = 25.0511 VDWAALS = -456.1658 EEL = 311.2027 HBOND = 0.0000 1-4 VDW = 32.8940 1-4 EEL = -1468.7435 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.5113E+03 6.4072E-01 7.2777E+00 Cl1 13 BOND = 10.5727 ANGLE = 36.0045 DIHED = 25.0331 VDWAALS = -456.3370 EEL = 308.4744 HBOND = 0.0000 1-4 VDW = 32.5244 1-4 EEL = -1467.5758 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.5113E+03 6.4072E-01 7.2777E+00 Cl1 13 BOND = 10.5727 ANGLE = 36.0045 DIHED = 25.0331 VDWAALS = -456.3370 EEL = 308.4744 HBOND = 0.0000 1-4 VDW = 32.5244 1-4 EEL = -1467.5758 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.02% of Total) | Build the list 0.02 (39.05% of List ) | Other 0.02 (60.95% of List ) | List time 0.04 ( 0.70% of Nonbo) | Short_ene time 2.47 (97.77% of Direc) | Other 0.06 ( 2.23% of Direc) | Direct Ewald time 2.53 (44.27% of Ewald) | Adjust Ewald time 0.16 ( 2.77% of Ewald) | Self Ewald time 0.00 ( 0.02% of Ewald) | Fill Bspline coeffs 0.07 ( 2.41% of Recip) | Fill charge grid 0.21 ( 7.09% of Recip) | Scalar sum 0.92 (30.47% of Recip) | Grad sum 0.39 (12.97% of Recip) | FFT time 1.41 (47.03% of Recip) | Other 0.00 ( 0.03% of Recip) | Recip Ewald time 3.00 (52.66% of Ewald) | Force Adjust 0.01 ( 0.16% of Ewald) | Virial junk 0.00 ( 0.07% of Ewald) | Start sycnronization 0.00 ( 0.01% of Ewald) | Other 0.00 ( 0.04% of Ewald) | Ewald time 5.70 (99.27% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) | Other 0.00 ( 0.02% of Nonbo) | Nonbond force 5.75 (97.20% of Force) | Bond/Angle/Dihedral 0.16 ( 2.76% of Force) | Other 0.00 ( 0.04% of Force) | Force time 5.91 (100.0% of Runmd) | Runmd Time 5.91 (99.45% of Total) | Other 0.03 ( 0.53% of Total) | Total time 5.94 (100.0% of ALL ) | Highest rstack allocated: 63292 | Highest istack allocated: 642 | Job began at 15:00:20.876 on 12/10/2009 | Setup done at 15:00:20.885 on 12/10/2009 | Run done at 15:00:26.820 on 12/10/2009 | wallclock() was called 38016 times