------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 02/06/2009 at 19:18:39 [-O]verwriting output File Assignments: | MDIN: equ.in | MDOUT: equ.out |INPCRD: n-dodecane.rst | PARM: n-dodecane.prmtop |RESTRT: n-dodecane.equ.rst | REFC: refc | MDVEL: n-dodecane.equ.mdvel | MDEN: n-dodecane.equ.mden | MDCRD: n-dodecane.equ.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: MD equilibration &cntrl imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1, ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500, ntwe=500, ntwv=500, cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0, vlimit=5, tempi=0.0, temp0=273.0, / -------------------------------------------------------------------------------- 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 = 16.668 | New format PARM file being parsed. | Version = 1.000 Date = 01/27/09 Time = 15:08:01 NATOM = 3800 NTYPES = 2 NBONH = 2600 MBONA = 1100 NTHETH = 6200 MTHETA = 1000 NPHIH = 9000 MPHIA = 2700 NHPARM = 0 NPARM = 0 NNB = 20900 NRES = 100 NBONA = 1100 NTHETA = 1000 NPHIA = 2700 NUMBND = 2 NUMANG = 3 NPTRA = 5 NATYP = 2 NPHB = 0 IFBOX = 1 NMXRS = 38 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 265402 | Hollerith 22902 | Integer 352008 | Max Pairs 2094429 | nblistReal 45600 | nblist Int 193164 | Total 12830 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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 = 500, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 500, ntwv = 500, ntwe = 500 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 = 9.82500, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 10000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 5.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 273.00000, tempi = 0.00000, tautp = 2.00000 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 = 33.335 Box Y = 33.335 Box Z = 33.335 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 9.825 Tol =0.100E-04 Ewald Coefficient = 0.28031 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00000007 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 = 1336379 | TOTAL SIZE OF NONBOND LIST = 1336379 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -796.8496 EKtot = 0.0000 EPtot = -796.8496 BOND = 14.2164 ANGLE = 110.5793 DIHED = 485.5095 1-4 NB = 400.9365 1-4 EEL = 370.9425 VDWAALS = -1782.7742 EELEC = -396.2596 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4393E-04 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 74.41 PRESS = 0.0 Etot = 140.9481 EKtot = 650.4080 EPtot = -509.4599 BOND = 31.8786 ANGLE = 183.7566 DIHED = 609.8334 1-4 NB = 432.8358 1-4 EEL = 372.8127 VDWAALS = -1742.3098 EELEC = -398.2672 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1455E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 114.07 PRESS = 0.0 Etot = 912.1005 EKtot = 997.0907 EPtot = -84.9902 BOND = 59.0755 ANGLE = 346.2104 DIHED = 740.7542 1-4 NB = 462.3707 1-4 EEL = 375.8227 VDWAALS = -1667.6965 EELEC = -401.5272 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3884E-03 ------------------------------------------------------------------------------ NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 147.72 PRESS = 0.0 Etot = 1521.7385 EKtot = 1291.1916 EPtot = 230.5469 BOND = 100.5583 ANGLE = 495.9533 DIHED = 816.1962 1-4 NB = 490.0672 1-4 EEL = 381.6663 VDWAALS = -1646.1081 EELEC = -407.7863 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3358E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 174.33 PRESS = 0.0 Etot = 2003.8198 EKtot = 1523.7620 EPtot = 480.0578 BOND = 129.3096 ANGLE = 707.9513 DIHED = 818.6928 1-4 NB = 490.4374 1-4 EEL = 382.3677 VDWAALS = -1639.8446 EELEC = -408.8564 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2801E-04 ------------------------------------------------------------------------------ NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 196.03 PRESS = 0.0 Etot = 2377.1478 EKtot = 1713.4211 EPtot = 663.7266 BOND = 163.4899 ANGLE = 834.8581 DIHED = 841.0020 1-4 NB = 498.1979 1-4 EEL = 386.5386 VDWAALS = -1647.9319 EELEC = -412.4280 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1479E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 215.32 PRESS = 0.0 Etot = 2672.8610 EKtot = 1882.0089 EPtot = 790.8521 BOND = 185.7532 ANGLE = 953.2393 DIHED = 819.1213 1-4 NB = 483.0290 1-4 EEL = 385.1494 VDWAALS = -1624.2973 EELEC = -411.1428 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5392E-04 ------------------------------------------------------------------------------ NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 224.94 PRESS = 0.0 Etot = 2908.2822 EKtot = 1966.1357 EPtot = 942.1466 BOND = 216.1490 ANGLE = 1061.9791 DIHED = 808.5047 1-4 NB = 507.3913 1-4 EEL = 387.7315 VDWAALS = -1625.7879 EELEC = -413.8212 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7251E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 234.55 PRESS = 0.0 Etot = 3097.4777 EKtot = 2050.1019 EPtot = 1047.3758 BOND = 239.6928 ANGLE = 1179.3976 DIHED = 827.9663 1-4 NB = 492.8705 1-4 EEL = 388.3601 VDWAALS = -1666.1831 EELEC = -414.7283 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8322E-04 ------------------------------------------------------------------------------ NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 240.48 PRESS = 0.0 Etot = 3251.1072 EKtot = 2101.9342 EPtot = 1149.1730 BOND = 277.1349 ANGLE = 1292.6844 DIHED = 819.4192 1-4 NB = 456.8172 1-4 EEL = 388.3230 VDWAALS = -1670.5893 EELEC = -414.6163 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1397E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 249.53 PRESS = 0.0 Etot = 3371.8260 EKtot = 2181.0749 EPtot = 1190.7511 BOND = 274.7845 ANGLE = 1310.0128 DIHED = 802.9234 1-4 NB = 490.7502 1-4 EEL = 390.5745 VDWAALS = -1660.9373 EELEC = -417.3569 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1928E-03 ------------------------------------------------------------------------------ NSTEP = 5500 TIME(PS) = 11.000 TEMP(K) = 254.96 PRESS = 0.0 Etot = 3471.0803 EKtot = 2228.5203 EPtot = 1242.5599 BOND = 265.9401 ANGLE = 1400.5494 DIHED = 782.2064 1-4 NB = 470.9605 1-4 EEL = 388.9254 VDWAALS = -1650.0619 EELEC = -415.9600 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4343E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 258.00 PRESS = 0.0 Etot = 3547.1254 EKtot = 2255.1067 EPtot = 1292.0187 BOND = 278.0118 ANGLE = 1424.2165 DIHED = 812.8563 1-4 NB = 489.1948 1-4 EEL = 391.3175 VDWAALS = -1685.6640 EELEC = -417.9142 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1558E-03 ------------------------------------------------------------------------------ NSTEP = 6500 TIME(PS) = 13.000 TEMP(K) = 263.78 PRESS = 0.0 Etot = 3606.0323 EKtot = 2305.6183 EPtot = 1300.4141 BOND = 291.9547 ANGLE = 1479.9193 DIHED = 769.2752 1-4 NB = 467.0184 1-4 EEL = 392.0182 VDWAALS = -1680.8426 EELEC = -418.9291 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1274E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 264.36 PRESS = 0.0 Etot = 3654.3400 EKtot = 2310.6455 EPtot = 1343.6945 BOND = 318.2849 ANGLE = 1495.9268 DIHED = 765.8723 1-4 NB = 470.9445 1-4 EEL = 393.4067 VDWAALS = -1681.0726 EELEC = -419.6680 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4414E-04 ------------------------------------------------------------------------------ NSTEP = 7500 TIME(PS) = 15.000 TEMP(K) = 261.91 PRESS = 0.0 Etot = 3697.6996 EKtot = 2289.2743 EPtot = 1408.4253 BOND = 324.2242 ANGLE = 1567.8460 DIHED = 768.2924 1-4 NB = 475.8729 1-4 EEL = 392.1931 VDWAALS = -1700.8950 EELEC = -419.1083 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1262E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 266.30 PRESS = 0.0 Etot = 3720.1727 EKtot = 2327.6777 EPtot = 1392.4950 BOND = 321.4033 ANGLE = 1560.3599 DIHED = 758.3612 1-4 NB = 462.8916 1-4 EEL = 393.0580 VDWAALS = -1684.0119 EELEC = -419.5671 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1678E-04 ------------------------------------------------------------------------------ NSTEP = 8500 TIME(PS) = 17.000 TEMP(K) = 270.76 PRESS = 0.0 Etot = 3738.9075 EKtot = 2366.6334 EPtot = 1372.2741 BOND = 306.2026 ANGLE = 1607.1865 DIHED = 727.2965 1-4 NB = 474.3771 1-4 EEL = 390.9943 VDWAALS = -1715.8366 EELEC = -417.9464 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1463E-03 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 271.85 PRESS = 0.0 Etot = 3756.1188 EKtot = 2376.1582 EPtot = 1379.9606 BOND = 347.9700 ANGLE = 1572.6906 DIHED = 739.3977 1-4 NB = 457.2913 1-4 EEL = 392.0034 VDWAALS = -1710.3375 EELEC = -419.0548 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.9185E-04 ------------------------------------------------------------------------------ NSTEP = 9500 TIME(PS) = 19.000 TEMP(K) = 268.14 PRESS = 0.0 Etot = 3770.5255 EKtot = 2343.6876 EPtot = 1426.8378 BOND = 318.7461 ANGLE = 1648.4610 DIHED = 720.4721 1-4 NB = 482.3279 1-4 EEL = 393.6863 VDWAALS = -1716.4008 EELEC = -420.4549 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5845E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 271.76 PRESS = 0.0 Etot = 3781.6217 EKtot = 2375.3459 EPtot = 1406.2759 BOND = 333.6484 ANGLE = 1641.0462 DIHED = 709.7888 1-4 NB = 460.7838 1-4 EEL = 392.9146 VDWAALS = -1712.0344 EELEC = -419.8716 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8896E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 10000 S T E P S NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 219.33 PRESS = 0.0 Etot = 2838.9654 EKtot = 1917.0624 EPtot = 921.9031 BOND = 231.4435 ANGLE = 1149.0927 DIHED = 768.9453 1-4 NB = 475.6347 1-4 EEL = 387.5178 VDWAALS = -1676.7880 EELEC = -413.9429 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1238E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 63.35 PRESS = 0.0 Etot = 1160.1706 EKtot = 553.7328 EPtot = 607.8402 BOND = 95.7462 ANGLE = 467.9301 DIHED = 69.8520 1-4 NB = 20.4176 1-4 EEL = 6.3481 VDWAALS = 37.0538 EELEC = 6.7647 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.9330E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Build the list 68.69 (99.54% of List ) | Other 0.32 ( 0.46% of List ) | List time 69.01 ( 5.58% of Nonbo) | Short_ene time 1022.20 (98.81% of Direc) | Other 12.30 ( 1.19% of Direc) | Direct Ewald time 1034.50 (88.67% of Ewald) | Adjust Ewald time 21.77 ( 1.87% of Ewald) | Fill Bspline coeffs 8.62 ( 8.56% of Recip) | Fill charge grid 12.33 (12.25% of Recip) | Scalar sum 22.18 (22.02% of Recip) | Grad sum 17.10 (16.98% of Recip) | FFT time 40.45 (40.17% of Recip) | Other 0.02 ( 0.02% of Recip) | Recip Ewald time 100.70 ( 8.63% of Ewald) | Force Adjust 8.61 ( 0.74% of Ewald) | Virial junk 1.05 ( 0.09% of Ewald) | Ewald time 1166.70 (94.41% of Nonbo) | Nonbond force 1235.74 (93.07% of Force) | Bond/Angle/Dihedral 91.89 ( 6.92% of Force) | Other 0.17 ( 0.01% of Force) | Force time 1327.80 (99.31% of Runmd) | Shake time 4.51 ( 0.34% of Runmd) | Verlet update time 4.71 ( 0.35% of Runmd) | Runmd Time 1337.05 (100.0% of Total) | Other 0.17 ( 0.01% of Total) | Total time 1337.24 (100.0% of ALL ) | Highest rstack allocated: 210838 | Highest istack allocated: 3800 | Job began at 19:18:39.143 on 02/06/2009 | Setup done at 19:18:39.360 on 02/06/2009 | Run done at 19:40:56.414 on 02/06/2009 | wallclock() was called 441374 times