------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 13:14:53 | 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.dhfr.CPU | INPCRD: md12.x | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short md, nve ensemble &cntrl ntx=7, irest=1, ntc=2, ntf=2, tol=0.0000001, nstlim=20, ntt=0, ntpr=1, ntwr=10000, dt=0.001, / &ewald NFFT1=72,NFFT2=64,NFFT3=60, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 27.261 | 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 = 22930 NTYPES = 17 NBONH = 21651 MBONA = 1302 NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140 NHPARM = 0 NPARM = 0 NNB = 41018 NRES = 6980 NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45 NUMANG = 91 NPTRA = 33 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 15 13 12 | Direct force subcell size = 4.6709 4.6571 4.5436 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 10000 iwrap = 0, ntwx = 0, 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 = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | 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 = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 70.063 Box Y = 60.543 Box Z = 54.523 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 64 NFFT3 = 60 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 510.050 ps Number of triangulated 3-point waters found: 6810 Sum of charges from parm topology file = -0.00000006 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 698255 | Integers 698786 | Nonbonded Pairs Initial Allocation: 3829883 -------------------------------------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP = 1 TIME(PS) = 510.051 TEMP(K) = 301.29 PRESS = 0.0 Etot = -57751.8144 EKtot = 14110.5279 EPtot = -71862.3423 BOND = 452.1690 ANGLE = 1277.0334 DIHED = 968.3542 1-4 NB = 545.9440 1-4 EEL = 6666.3920 VDWAALS = 8109.3892 EELEC = -89881.6242 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3231E-04 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 510.052 TEMP(K) = 301.16 PRESS = 0.0 Etot = -57751.8172 EKtot = 14104.5361 EPtot = -71856.3532 BOND = 454.7406 ANGLE = 1280.2592 DIHED = 969.1509 1-4 NB = 547.4649 1-4 EEL = 6661.7833 VDWAALS = 8112.2875 EELEC = -89882.0395 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2113E-04 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 510.053 TEMP(K) = 300.92 PRESS = 0.0 Etot = -57751.8458 EKtot = 14093.2466 EPtot = -71845.0923 BOND = 459.7257 ANGLE = 1284.1223 DIHED = 971.1727 1-4 NB = 549.0250 1-4 EEL = 6656.3558 VDWAALS = 8116.0426 EELEC = -89881.5364 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3093E-04 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 510.054 TEMP(K) = 300.56 PRESS = 0.0 Etot = -57751.9322 EKtot = 14076.6171 EPtot = -71828.5493 BOND = 466.5030 ANGLE = 1288.5461 DIHED = 974.2466 1-4 NB = 550.4298 1-4 EEL = 6650.2845 VDWAALS = 8120.4455 EELEC = -89879.0048 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5802E-04 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 510.055 TEMP(K) = 300.11 PRESS = 0.0 Etot = -57751.8238 EKtot = 14055.5431 EPtot = -71807.3668 BOND = 474.1741 ANGLE = 1293.2730 DIHED = 978.0262 1-4 NB = 551.4584 1-4 EEL = 6643.7780 VDWAALS = 8125.2689 EELEC = -89873.3454 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4721E-04 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 510.056 TEMP(K) = 299.61 PRESS = 0.0 Etot = -57751.6541 EKtot = 14031.8307 EPtot = -71783.4849 BOND = 481.6902 ANGLE = 1297.7743 DIHED = 982.0527 1-4 NB = 551.9190 1-4 EEL = 6637.0660 VDWAALS = 8130.5916 EELEC = -89864.5786 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6757E-04 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 510.057 TEMP(K) = 299.10 PRESS = 0.0 Etot = -57751.4692 EKtot = 14007.9494 EPtot = -71759.4186 BOND = 488.0154 ANGLE = 1301.2367 DIHED = 985.8347 1-4 NB = 551.7040 1-4 EEL = 6630.3791 VDWAALS = 8136.0515 EELEC = -89852.6399 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7841E-04 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 510.058 TEMP(K) = 298.64 PRESS = 0.0 Etot = -57751.4377 EKtot = 13986.5733 EPtot = -71738.0111 BOND = 492.3144 ANGLE = 1302.7119 DIHED = 988.9237 1-4 NB = 550.8103 1-4 EEL = 6623.9284 VDWAALS = 8141.6820 EELEC = -89838.3817 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1148E-03 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 510.059 TEMP(K) = 298.29 PRESS = 0.0 Etot = -57751.4687 EKtot = 13969.9704 EPtot = -71721.4391 BOND = 494.1352 ANGLE = 1301.4406 DIHED = 990.9727 1-4 NB = 549.3279 1-4 EEL = 6617.8892 VDWAALS = 8147.4573 EELEC = -89822.6621 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1363E-03 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 510.060 TEMP(K) = 298.06 PRESS = 0.0 Etot = -57751.5457 EKtot = 13959.3933 EPtot = -71710.9390 BOND = 493.5409 ANGLE = 1297.2411 DIHED = 991.7769 1-4 NB = 547.4171 1-4 EEL = 6612.3958 VDWAALS = 8153.5158 EELEC = -89806.8266 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1395E-03 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 510.061 TEMP(K) = 297.96 PRESS = 0.0 Etot = -57751.6765 EKtot = 13954.7138 EPtot = -71706.3903 BOND = 491.1306 ANGLE = 1290.7681 DIHED = 991.3002 1-4 NB = 545.2822 1-4 EEL = 6607.5450 VDWAALS = 8160.0074 EELEC = -89792.4237 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1356E-03 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 510.062 TEMP(K) = 297.96 PRESS = 0.0 Etot = -57751.9280 EKtot = 13954.4857 EPtot = -71706.4137 BOND = 487.9040 ANGLE = 1283.4713 DIHED = 989.6788 1-4 NB = 543.1406 1-4 EEL = 6603.4075 VDWAALS = 8166.9816 EELEC = -89780.9975 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1420E-03 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 510.063 TEMP(K) = 298.00 PRESS = 0.0 Etot = -57752.0165 EKtot = 13956.5073 EPtot = -71708.5238 BOND = 484.9715 ANGLE = 1277.2170 DIHED = 987.1954 1-4 NB = 541.1827 1-4 EEL = 6600.0426 VDWAALS = 8174.5348 EELEC = -89773.6677 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1312E-03 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 510.064 TEMP(K) = 298.05 PRESS = 0.0 Etot = -57751.9433 EKtot = 13958.6873 EPtot = -71710.6306 BOND = 483.1834 ANGLE = 1273.6992 DIHED = 984.2295 1-4 NB = 539.5328 1-4 EEL = 6597.5101 VDWAALS = 8182.6368 EELEC = -89771.4223 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1069E-03 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 510.065 TEMP(K) = 298.07 PRESS = 0.0 Etot = -57751.8757 EKtot = 13959.8598 EPtot = -71711.7355 BOND = 482.8154 ANGLE = 1273.8740 DIHED = 981.2027 1-4 NB = 538.2293 1-4 EEL = 6595.8748 VDWAALS = 8191.2742 EELEC = -89775.0059 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1019E-03 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 510.066 TEMP(K) = 298.08 PRESS = 0.0 Etot = -57751.7345 EKtot = 13960.1845 EPtot = -71711.9191 BOND = 483.4601 ANGLE = 1277.6514 DIHED = 978.5324 1-4 NB = 537.2351 1-4 EEL = 6595.1998 VDWAALS = 8200.3602 EELEC = -89784.3581 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8973E-04 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 510.067 TEMP(K) = 298.09 PRESS = 0.0 Etot = -57751.6639 EKtot = 13960.9166 EPtot = -71712.5805 BOND = 484.2038 ANGLE = 1283.9786 DIHED = 976.5876 1-4 NB = 536.4720 1-4 EEL = 6595.5301 VDWAALS = 8209.7526 EELEC = -89799.1052 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8263E-04 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 510.068 TEMP(K) = 298.15 PRESS = 0.0 Etot = -57751.7250 EKtot = 13963.6665 EPtot = -71715.3914 BOND = 484.0457 ANGLE = 1291.2696 DIHED = 975.6400 1-4 NB = 535.8588 1-4 EEL = 6596.8725 VDWAALS = 8219.2259 EELEC = -89818.3040 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8328E-04 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 510.069 TEMP(K) = 298.28 PRESS = 0.0 Etot = -57751.7544 EKtot = 13969.5163 EPtot = -71721.2707 BOND = 482.3871 ANGLE = 1297.9749 DIHED = 975.8145 1-4 NB = 535.3299 1-4 EEL = 6599.1784 VDWAALS = 8228.6736 EELEC = -89840.6291 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1039E-03 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 298.47 PRESS = 0.0 Etot = -57751.7266 EKtot = 13978.4173 EPtot = -71730.1439 BOND = 479.3669 ANGLE = 1303.0252 DIHED = 977.0605 1-4 NB = 534.8304 1-4 EEL = 6602.3385 VDWAALS = 8237.3235 EELEC = -89864.0889 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8686E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 298.94 PRESS = 0.0 Etot = -57751.7427 EKtot = 14000.6571 EPtot = -71752.3998 BOND = 480.0239 ANGLE = 1288.8284 DIHED = 980.8876 1-4 NB = 544.1297 1-4 EEL = 6619.6876 VDWAALS = 8163.1751 EELEC = -89829.1321 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8952E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 1.17 PRESS = 0.0 Etot = 0.1631 EKtot = 54.6594 EPtot = 54.6896 BOND = 12.0891 ANGLE = 9.9261 DIHED = 7.3516 1-4 NB = 6.0734 1-4 EEL = 24.0705 VDWAALS = 39.6044 EELEC = 40.3457 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 0.1870 Ewald error estimate: 0.3707E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 2.61 90.77 | Bond 0.00 0.03 | Angle 0.01 0.42 | Dihedral 0.05 1.71 | Shake 0.03 0.94 | RunMD 0.18 6.13 | Other 0.00 0.00 | ------------------------------ | Total 2.87 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.10 | Build List 0.27 9.40 | --------------------------------- | Total 0.27 9.51 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 1.80 62.71 | Exclude Masked 0.04 1.29 | Other 0.01 0.49 | --------------------------------- | Total 1.85 64.48 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.04 1.46 | Grid Charges 0.05 1.71 | Scalar Sum 0.08 2.92 | Gradient Sum 0.08 2.65 | FFT 0.23 8.04 | --------------------------------- | Total 0.48 16.78 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 2.72 Per Step(ms) = 143.07 | ns/day = 0.60 seconds/ns = 143065.69 | | Average timings for all steps: | Elapsed(s) = 2.95 Per Step(ms) = 147.63 | ns/day = 0.59 seconds/ns = 147629.15 | ----------------------------------------------------- | Setup CPU time: 0.22 seconds | NonSetup CPU time: 2.87 seconds | Total CPU time: 3.09 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 3 seconds | Total wall time: 4 seconds 0.00 hours