------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 14:32:32 | WARNING: Stack usage limited by a hard resource limit of 536870912 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.ips_ntt3 | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: check of isotropic periodic sum simulation, ntb=2 &cntrl imin=0, ntx=5, ntpr=1, nscm=5000,iwrap=1, ntf=2, ntc=2, ntb=2, ntp=1, tautp=5.0, taup=5.0, nstlim=20, t=0.0, dt=0.002, cut=12.0, ntt=3,gamma_ln=2.0, irest=1 ips=1, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 27.755 | INFO: Old style PARM file read | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 24030 NTYPES = 18 NBONH = 23393 MBONA = 682 NTHETH = 805 MTHETA = 1049 NPHIH = 1416 MPHIA = 1695 NHPARM = 0 NPARM = 0 NNB = 36045 NRES = 7742 NBONA = 682 NTHETA = 1049 NPHIA = 1695 NUMBND = 39 NUMANG = 76 NPTRA = 34 NATYP = 28 NPHB = 1 IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 9 9 9 | Direct force subcell size = 7.5538 7.5538 7.5538 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 5000, 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= 2.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 0 vdwmeth = 2, eedmeth = 6, netfrc = 1 Box X = 67.985 Box Y = 67.985 Box Z = 67.985 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 72 NFFT2 = 72 NFFT3 = 72 Cutoff= 12.000 Tol =0.100E-04 Ewald Coefficient = 0.22664 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 7684 Sum of charges from parm topology file = 0.00000017 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 873759 | Integers 631705 | Nonbonded Pairs Initial Allocation: 11950719 ---------------------------------- Using 3D-IPS algorithm IPS Radius: 12.00 A Using IPS for electrostatic energy Using IPS for L-J energy ---------------------------------- -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=6: Using IPS method for electrostatic energy | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.27 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.78 |--------------------------------------------------- NSTEP = 1 TIME(PS) = 0.002 TEMP(K) = 301.35 PRESS = -135.9 Etot = -67870.4857 EKtot = 14580.9568 EPtot = -82451.4425 BOND = 236.3050 ANGLE = 523.8042 DIHED = 542.6053 1-4 NB = 264.7708 1-4 EEL = -3290.5712 VDWAALS = 10291.7291 EELEC = -91020.0857 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6966.9758 VIRIAL = 7676.7858 VOLUME = 241885.2000 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 0.004 TEMP(K) = 300.66 PRESS = -121.0 Etot = -67873.8874 EKtot = 14547.2454 EPtot = -82421.1328 BOND = 232.5905 ANGLE = 524.6147 DIHED = 538.0261 1-4 NB = 266.0633 1-4 EEL = -3296.3577 VDWAALS = 10297.6253 EELEC = -90983.6950 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6957.2969 VIRIAL = 7589.2134 VOLUME = 241884.6092 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 0.006 TEMP(K) = 299.85 PRESS = -108.9 Etot = -67875.0567 EKtot = 14508.0456 EPtot = -82383.1023 BOND = 238.3970 ANGLE = 517.7237 DIHED = 533.3168 1-4 NB = 265.8476 1-4 EEL = -3299.1309 VDWAALS = 10304.3811 EELEC = -90943.6377 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6951.8308 VIRIAL = 7520.7062 VOLUME = 241884.0827 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 0.008 TEMP(K) = 299.36 PRESS = -105.7 Etot = -67863.9013 EKtot = 14484.4273 EPtot = -82348.3285 BOND = 246.9647 ANGLE = 506.6171 DIHED = 529.8718 1-4 NB = 263.9773 1-4 EEL = -3298.4815 VDWAALS = 10311.3001 EELEC = -90908.5780 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6947.4963 VIRIAL = 7499.7308 VOLUME = 241883.6084 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 0.010 TEMP(K) = 298.89 PRESS = -106.7 Etot = -67852.7104 EKtot = 14461.6924 EPtot = -82314.4028 BOND = 247.8713 ANGLE = 501.1680 DIHED = 528.6978 1-4 NB = 260.7972 1-4 EEL = -3294.6320 VDWAALS = 10319.4266 EELEC = -90877.7317 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6951.8054 VIRIAL = 7508.9563 VOLUME = 241883.1478 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 0.012 TEMP(K) = 298.50 PRESS = -112.5 Etot = -67845.8988 EKtot = 14442.9691 EPtot = -82288.8679 BOND = 239.6405 ANGLE = 502.2310 DIHED = 529.1519 1-4 NB = 257.2501 1-4 EEL = -3287.8824 VDWAALS = 10329.3101 EELEC = -90858.5692 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6947.2653 VIRIAL = 7534.8781 VOLUME = 241882.6831 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 0.014 TEMP(K) = 298.15 PRESS = -118.1 Etot = -67837.3788 EKtot = 14426.2154 EPtot = -82263.5942 BOND = 231.4396 ANGLE = 508.8802 DIHED = 530.7933 1-4 NB = 254.8020 1-4 EEL = -3279.0101 VDWAALS = 10342.5123 EELEC = -90853.0115 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6942.1439 VIRIAL = 7558.8687 VOLUME = 241882.1933 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 0.016 TEMP(K) = 297.69 PRESS = -118.5 Etot = -67835.6303 EKtot = 14403.9607 EPtot = -82239.5910 BOND = 229.1865 ANGLE = 514.1669 DIHED = 532.2263 1-4 NB = 253.7218 1-4 EEL = -3268.9347 VDWAALS = 10359.2179 EELEC = -90859.1756 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6948.1384 VIRIAL = 7566.8481 VOLUME = 241881.6794 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 0.018 TEMP(K) = 297.52 PRESS = -117.2 Etot = -67834.6065 EKtot = 14395.3292 EPtot = -82229.9356 BOND = 231.6018 ANGLE = 512.8557 DIHED = 533.5740 1-4 NB = 253.4300 1-4 EEL = -3259.9738 VDWAALS = 10377.9988 EELEC = -90879.4221 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6950.5003 VIRIAL = 7562.5312 VOLUME = 241881.1638 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 297.67 PRESS = -105.8 Etot = -67831.5963 EKtot = 14403.0221 EPtot = -82234.6184 BOND = 229.2622 ANGLE = 504.7687 DIHED = 535.1422 1-4 NB = 253.3929 1-4 EEL = -3252.8817 VDWAALS = 10397.4160 EELEC = -90901.7186 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6944.7243 VIRIAL = 7497.3287 VOLUME = 241880.6538 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 0.022 TEMP(K) = 297.68 PRESS = -78.9 Etot = -67835.8757 EKtot = 14403.1683 EPtot = -82239.0440 BOND = 225.1374 ANGLE = 499.3442 DIHED = 536.8623 1-4 NB = 253.9350 1-4 EEL = -3250.3396 VDWAALS = 10415.2405 EELEC = -90919.2237 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6943.1539 VIRIAL = 7355.4102 VOLUME = 241880.1929 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 0.024 TEMP(K) = 297.50 PRESS = -42.2 Etot = -67844.2225 EKtot = 14394.7520 EPtot = -82238.9745 BOND = 223.5139 ANGLE = 499.4560 DIHED = 537.3836 1-4 NB = 255.1098 1-4 EEL = -3252.1081 VDWAALS = 10430.3728 EELEC = -90932.7024 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6936.4500 VIRIAL = 7156.6154 VOLUME = 241879.8480 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 0.026 TEMP(K) = 297.58 PRESS = -2.9 Etot = -67840.3021 EKtot = 14398.2607 EPtot = -82238.5628 BOND = 225.6998 ANGLE = 502.3446 DIHED = 536.3876 1-4 NB = 256.3855 1-4 EEL = -3257.0953 VDWAALS = 10444.2934 EELEC = -90946.5786 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6920.0885 VIRIAL = 6935.3888 VOLUME = 241879.6617 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 0.028 TEMP(K) = 297.81 PRESS = 36.4 Etot = -67837.1225 EKtot = 14409.4958 EPtot = -82246.6183 BOND = 233.1438 ANGLE = 504.1916 DIHED = 533.8280 1-4 NB = 256.8303 1-4 EEL = -3263.4095 VDWAALS = 10456.7029 EELEC = -90967.9054 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6927.6300 VIRIAL = 6737.4339 VOLUME = 241879.6448 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 0.030 TEMP(K) = 298.21 PRESS = 62.3 Etot = -67833.0842 EKtot = 14429.1227 EPtot = -82262.2069 BOND = 242.2996 ANGLE = 502.2143 DIHED = 530.9208 1-4 NB = 255.6360 1-4 EEL = -3269.4634 VDWAALS = 10467.0181 EELEC = -90990.8323 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6916.1678 VIRIAL = 6590.9343 VOLUME = 241879.7976 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 0.032 TEMP(K) = 298.80 PRESS = 77.6 Etot = -67826.1043 EKtot = 14457.4608 EPtot = -82283.5651 BOND = 251.1717 ANGLE = 496.7936 DIHED = 529.5599 1-4 NB = 253.5618 1-4 EEL = -3274.4791 VDWAALS = 10474.5590 EELEC = -91014.7320 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6929.1702 VIRIAL = 6523.8725 VOLUME = 241880.0620 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 0.034 TEMP(K) = 299.06 PRESS = 77.6 Etot = -67833.3039 EKtot = 14469.8708 EPtot = -82303.1747 BOND = 258.3089 ANGLE = 492.2323 DIHED = 530.0653 1-4 NB = 251.2401 1-4 EEL = -3278.5009 VDWAALS = 10477.3894 EELEC = -91033.9099 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6919.5727 VIRIAL = 6514.4778 VOLUME = 241880.3926 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 0.036 TEMP(K) = 299.02 PRESS = 68.4 Etot = -67839.1680 EKtot = 14468.1919 EPtot = -82307.3599 BOND = 260.5184 ANGLE = 494.3700 DIHED = 533.5749 1-4 NB = 249.2234 1-4 EEL = -3282.0586 VDWAALS = 10475.9404 EELEC = -91038.9285 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6896.4680 VIRIAL = 6539.2154 VOLUME = 241880.7230 Density = 1.0205 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 0.038 TEMP(K) = 299.01 PRESS = 63.4 Etot = -67831.3532 EKtot = 14467.5137 EPtot = -82298.8669 BOND = 257.3186 ANGLE = 500.6704 DIHED = 538.1738 1-4 NB = 248.1102 1-4 EEL = -3285.1235 VDWAALS = 10472.5536 EELEC = -91030.5699 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6898.0779 VIRIAL = 6566.7468 VOLUME = 241881.0139 Density = 1.0205 ------------------------------------------------------------------------------ wrapping first mol.: -45.32282 32.04808 55.50889 NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 298.81 PRESS = 55.8 Etot = -67818.6520 EKtot = 14457.7273 EPtot = -82276.3794 BOND = 254.8151 ANGLE = 505.5912 DIHED = 542.9031 1-4 NB = 247.4472 1-4 EEL = -3288.1101 VDWAALS = 10467.6539 EELEC = -91006.6799 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6904.9540 VIRIAL = 6613.4768 VOLUME = 241881.2833 Density = 1.0205 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 298.66 PRESS = -41.6 Etot = -67843.0170 EKtot = 14450.4714 EPtot = -82293.4884 BOND = 239.7593 ANGLE = 505.7019 DIHED = 534.1533 1-4 NB = 256.0766 1-4 EEL = -3276.4272 VDWAALS = 10395.6321 EELEC = -90948.3844 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 6934.9955 VIRIAL = 7152.4709 VOLUME = 241881.5821 Density = 1.0205 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = 1.04 PRESS = 82.3 Etot = 15.6175 EKtot = 50.1849 EPtot = 61.9988 BOND = 11.6330 ANGLE = 8.7087 DIHED = 4.1276 1-4 NB = 5.4738 1-4 EEL = 15.9142 VDWAALS = 68.4688 EELEC = 62.6065 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 19.5870 VIRIAL = 447.5960 VOLUME = 1.7049 Density = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 8.65 97.74 | Bond 0.00 0.01 | Angle 0.00 0.03 | Dihedral 0.01 0.08 | Shake 0.02 0.26 | RunMD 0.17 1.88 | Other 0.00 0.00 | ------------------------------ | Total 8.85 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.05 | Build List 1.13 12.79 | --------------------------------- | Total 1.14 12.83 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 7.47 84.43 | Exclude Masked 0.00 0.00 | Other 0.04 0.47 | --------------------------------- | Total 7.52 84.91 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.00 0.00 | Scalar Sum 0.00 0.00 | Gradient Sum 0.00 0.00 | FFT 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 8.25 Per Step(ms) = 434.26 | ns/day = 0.40 seconds/ns = 217130.32 | | Average timings for all steps: | Elapsed(s) = 8.87 Per Step(ms) = 443.45 | ns/day = 0.39 seconds/ns = 221724.65 | ----------------------------------------------------- | Setup CPU time: 0.10 seconds | NonSetup CPU time: 8.85 seconds | Total CPU time: 8.95 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 9 seconds | Total wall time: 9 seconds 0.00 hours