------------------------------------------------------- Amber 18 PMEMD 2018 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 18 | Run on 05/16/2019 at 12:17:33 | Executable path: /home/new/amberg/amber18/bin/pmemd | Working directory: /home/new/amber-test-i/test-3npo/3npo-nvt-elec-field | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: md-prod-nvt-ef-new-1.in | MDOUT: md-prod-nvt-ef-new-1.out | INPCRD: md-prod-nvt-1.ncrst | PARM: sys.prmtop | RESTRT: md-prod-nvt-ef-new-1.ncrst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: md-prod-nvt-ef-new-1.nc | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: Production simulation NVT ensemble &cntrl imin = 0, irest = 1, ntx = 5, ntb = 1, cut = 9.0, ntr = 0, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, ig = -1, iwrap = 1, efx = 0, efy = 0, efz = 300, efn = 1, nstlim = 20000, dt = 0.002, ntpr = 1000, ntwx = 2000, ntwr = 2000 / &ewald nfft1=64, nfft2=64, nfft3=64, / Note: ig = -1. Setting random seed to 422250 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | Largest sphere to fit in unit cell has radius = 32.139 | New format PARM file being parsed. | Version = 1.000 Date = 05/06/19 Time = 11:29:34 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting box info from netcdf restart file NATOM = 26575 NTYPES = 17 NBONH = 25287 MBONA = 1301 NTHETH = 3005 MTHETA = 1762 NPHIH = 5877 MPHIA = 5675 NHPARM = 0 NPARM = 0 NNB = 46378 NRES = 8163 NBONA = 1301 NTHETA = 1762 NPHIA = 5675 NUMBND = 67 NUMANG = 152 NPTRA = 191 NATYP = 36 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 12 12 12 | Direct force subcell size = 5.3565 5.3565 5.3565 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 1000, ntrx = 1, ntwr = 2000 iwrap = 1, ntwx = 2000, ntwv = 0, ntwe = 0 ioutfm = 1, 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 = 9.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 422250 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 64.278 Box Y = 64.278 Box Z = 64.278 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 64 NFFT2 = 64 NFFT3 = 64 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 540.000 ps Number of triangulated 3-point waters found: 7993 Sum of charges from parm topology file = -0.00000008 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 800638 | Integers 979103 | Nonbonded Pairs Initial Allocation: 6059100 -------------------------------------------------------------------------------- 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 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.39 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.84 |--------------------------------------------------- NSTEP = 1000 TIME(PS) = 542.000 TEMP(K) = 335.03 PRESS = 0.0 Etot = -74942.0393 EKtot = 18121.3234 EPtot = -93063.3627 BOND = 509.1732 ANGLE = 1419.1543 DIHED = 2164.9503 1-4 NB = 571.3092 1-4 EEL = 8343.6757 VDWAALS = 8960.7736 EELEC = -100107.9008 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -14924.4982 Ewald error estimate: 0.6480E-05 ------------------------------------------------------------------------------ NSTEP = 2000 TIME(PS) = 544.000 TEMP(K) = 307.38 PRESS = 0.0 Etot = -79497.6155 EKtot = 16625.9914 EPtot = -96123.6069 BOND = 504.2760 ANGLE = 1339.1304 DIHED = 2167.2823 1-4 NB = 573.6740 1-4 EEL = 8409.0452 VDWAALS = 9538.4000 EELEC = -103080.7334 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -15574.6813 Ewald error estimate: 0.2367E-03 ------------------------------------------------------------------------------ NSTEP = 3000 TIME(PS) = 546.000 TEMP(K) = 303.07 PRESS = 0.0 Etot = -80743.5876 EKtot = 16392.9119 EPtot = -97136.4995 BOND = 482.7689 ANGLE = 1392.5923 DIHED = 2138.6875 1-4 NB = 588.7623 1-4 EEL = 8389.2526 VDWAALS = 9485.5940 EELEC = -103777.6186 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -15836.5386 Ewald error estimate: 0.3006E-04 ------------------------------------------------------------------------------ NSTEP = 4000 TIME(PS) = 548.000 TEMP(K) = 300.12 PRESS = 0.0 Etot = -81367.9670 EKtot = 16233.4947 EPtot = -97601.4617 BOND = 516.4642 ANGLE = 1386.4459 DIHED = 2193.2303 1-4 NB = 568.8674 1-4 EEL = 8331.9041 VDWAALS = 9865.9068 EELEC = -104392.3821 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16071.8984 Ewald error estimate: 0.1295E-03 ------------------------------------------------------------------------------ NSTEP = 5000 TIME(PS) = 550.000 TEMP(K) = 303.31 PRESS = 0.0 Etot = -81219.4994 EKtot = 16405.5942 EPtot = -97625.0936 BOND = 487.9114 ANGLE = 1438.5582 DIHED = 2212.8176 1-4 NB = 571.9317 1-4 EEL = 8334.4597 VDWAALS = 9748.0132 EELEC = -104226.5862 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16192.1992 Ewald error estimate: 0.6642E-04 ------------------------------------------------------------------------------ NSTEP = 6000 TIME(PS) = 552.000 TEMP(K) = 298.71 PRESS = 0.0 Etot = -81556.6208 EKtot = 16156.9124 EPtot = -97713.5332 BOND = 499.4588 ANGLE = 1378.9147 DIHED = 2159.7188 1-4 NB = 569.1410 1-4 EEL = 8310.4449 VDWAALS = 9538.0064 EELEC = -103881.8525 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16287.3653 Ewald error estimate: 0.1780E-03 ------------------------------------------------------------------------------ NSTEP = 7000 TIME(PS) = 554.000 TEMP(K) = 301.84 PRESS = 0.0 Etot = -81606.4663 EKtot = 16326.2094 EPtot = -97932.6757 BOND = 535.7540 ANGLE = 1400.0063 DIHED = 2185.4143 1-4 NB = 565.1438 1-4 EEL = 8302.0765 VDWAALS = 9468.1070 EELEC = -103934.8790 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16454.2985 Ewald error estimate: 0.1921E-03 ------------------------------------------------------------------------------ NSTEP = 8000 TIME(PS) = 556.000 TEMP(K) = 301.66 PRESS = 0.0 Etot = -81948.5576 EKtot = 16316.7903 EPtot = -98265.3478 BOND = 513.3986 ANGLE = 1414.2451 DIHED = 2168.8689 1-4 NB = 579.1926 1-4 EEL = 8360.9527 VDWAALS = 9730.6266 EELEC = -104360.7435 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16671.8887 Ewald error estimate: 0.1776E-03 ------------------------------------------------------------------------------ NSTEP = 9000 TIME(PS) = 558.000 TEMP(K) = 301.57 PRESS = 0.0 Etot = -82045.8286 EKtot = 16311.4917 EPtot = -98357.3202 BOND = 534.5800 ANGLE = 1455.6951 DIHED = 2208.3997 1-4 NB = 550.6123 1-4 EEL = 8310.2101 VDWAALS = 9738.9924 EELEC = -104365.5822 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16790.2276 Ewald error estimate: 0.5997E-04 ------------------------------------------------------------------------------ NSTEP = 10000 TIME(PS) = 560.000 TEMP(K) = 298.19 PRESS = 0.0 Etot = -82143.6344 EKtot = 16128.9117 EPtot = -98272.5461 BOND = 487.6068 ANGLE = 1450.9147 DIHED = 2159.7992 1-4 NB = 576.2511 1-4 EEL = 8312.9457 VDWAALS = 9647.6033 EELEC = -104075.7840 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16831.8830 Ewald error estimate: 0.1558E-03 ------------------------------------------------------------------------------ NSTEP = 11000 TIME(PS) = 562.000 TEMP(K) = 297.21 PRESS = 0.0 Etot = -82342.7033 EKtot = 16075.8050 EPtot = -98418.5083 BOND = 529.2571 ANGLE = 1452.1053 DIHED = 2196.9955 1-4 NB = 560.2932 1-4 EEL = 8285.8937 VDWAALS = 9629.4443 EELEC = -104131.9148 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16940.5826 Ewald error estimate: 0.2414E-03 ------------------------------------------------------------------------------ NSTEP = 12000 TIME(PS) = 564.000 TEMP(K) = 300.02 PRESS = 0.0 Etot = -82327.8484 EKtot = 16228.0883 EPtot = -98555.9366 BOND = 512.8903 ANGLE = 1396.9171 DIHED = 2184.1461 1-4 NB = 585.6456 1-4 EEL = 8304.1541 VDWAALS = 9794.5008 EELEC = -104323.9927 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17010.1980 Ewald error estimate: 0.1606E-03 ------------------------------------------------------------------------------ NSTEP = 13000 TIME(PS) = 566.000 TEMP(K) = 299.04 PRESS = 0.0 Etot = -82683.4066 EKtot = 16174.6234 EPtot = -98858.0300 BOND = 521.6159 ANGLE = 1439.6546 DIHED = 2221.8928 1-4 NB = 552.3670 1-4 EEL = 8307.0544 VDWAALS = 10105.4342 EELEC = -104865.2325 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17140.8164 Ewald error estimate: 0.1310E-03 ------------------------------------------------------------------------------ NSTEP = 14000 TIME(PS) = 568.000 TEMP(K) = 299.64 PRESS = 0.0 Etot = -82812.2473 EKtot = 16207.4671 EPtot = -99019.7144 BOND = 505.3324 ANGLE = 1444.7280 DIHED = 2194.4625 1-4 NB = 549.9565 1-4 EEL = 8268.0808 VDWAALS = 9950.5293 EELEC = -104658.7997 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17274.0042 Ewald error estimate: 0.7392E-04 ------------------------------------------------------------------------------ NSTEP = 15000 TIME(PS) = 570.000 TEMP(K) = 298.88 PRESS = 0.0 Etot = -82959.6630 EKtot = 16166.3163 EPtot = -99125.9793 BOND = 499.1668 ANGLE = 1442.3660 DIHED = 2219.5211 1-4 NB = 552.3057 1-4 EEL = 8273.6508 VDWAALS = 9948.3366 EELEC = -104678.4160 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17382.9103 Ewald error estimate: 0.1583E-03 ------------------------------------------------------------------------------ NSTEP = 16000 TIME(PS) = 572.000 TEMP(K) = 299.57 PRESS = 0.0 Etot = -82811.6354 EKtot = 16203.4427 EPtot = -99015.0781 BOND = 483.3462 ANGLE = 1406.5639 DIHED = 2176.1377 1-4 NB = 557.4273 1-4 EEL = 8305.9547 VDWAALS = 9630.9781 EELEC = -104112.2271 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17463.2590 Ewald error estimate: 0.1281E-03 ------------------------------------------------------------------------------ NSTEP = 17000 TIME(PS) = 574.000 TEMP(K) = 300.01 PRESS = 0.0 Etot = -82977.5230 EKtot = 16227.1702 EPtot = -99204.6932 BOND = 486.3295 ANGLE = 1434.8554 DIHED = 2200.2326 1-4 NB = 549.9538 1-4 EEL = 8304.0862 VDWAALS = 9796.1898 EELEC = -104378.7325 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17597.6080 Ewald error estimate: 0.1009E-03 ------------------------------------------------------------------------------ NSTEP = 18000 TIME(PS) = 576.000 TEMP(K) = 299.19 PRESS = 0.0 Etot = -83099.5624 EKtot = 16183.0572 EPtot = -99282.6196 BOND = 556.9179 ANGLE = 1369.3136 DIHED = 2207.7121 1-4 NB = 568.9872 1-4 EEL = 8316.7032 VDWAALS = 9710.0020 EELEC = -104425.7499 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17586.5058 Ewald error estimate: 0.1223E-03 ------------------------------------------------------------------------------ NSTEP = 19000 TIME(PS) = 578.000 TEMP(K) = 303.16 PRESS = 0.0 Etot = -82855.7699 EKtot = 16397.7745 EPtot = -99253.5444 BOND = 506.1377 ANGLE = 1440.8106 DIHED = 2190.0264 1-4 NB = 541.5077 1-4 EEL = 8305.4628 VDWAALS = 9718.2781 EELEC = -104239.3199 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17716.4478 Ewald error estimate: 0.5262E-04 ------------------------------------------------------------------------------ NSTEP = 20000 TIME(PS) = 580.000 TEMP(K) = 298.88 PRESS = 0.0 Etot = -83123.4329 EKtot = 16166.2096 EPtot = -99289.6425 BOND = 529.6325 ANGLE = 1411.2702 DIHED = 2176.7437 1-4 NB = 547.6487 1-4 EEL = 8275.2716 VDWAALS = 9754.0688 EELEC = -104178.7631 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -17805.5148 Ewald error estimate: 0.2400E-03 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20000 TIME(PS) = 580.000 TEMP(K) = 302.32 PRESS = 0.0 Etot = -81753.2804 EKtot = 16352.4793 EPtot = -98105.7597 BOND = 510.1009 ANGLE = 1415.7121 DIHED = 2186.3520 1-4 NB = 564.0489 1-4 EEL = 8317.5640 VDWAALS = 9687.9893 EELEC = -104009.8605 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = -16777.6663 Ewald error estimate: 0.1321E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20000 TIME(PS) = 580.000 TEMP(K) = 7.84 PRESS = 0.0 Etot = 1801.5803 EKtot = 424.0761 EPtot = 1413.5228 BOND = 19.6490 ANGLE = 31.0534 DIHED = 21.7425 1-4 NB = 13.0859 1-4 EEL = 35.2505 VDWAALS = 229.2162 EELEC = 967.6214 EHBOND = 0.0000 RESTRAINT = 0.0000 ELECTRIC_FIELD = 759.1694 Ewald error estimate: 0.6740E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1694.56 92.09 | Bond 0.26 0.01 | Angle 5.21 0.28 | Dihedral 30.07 1.63 | Shake 14.48 0.79 | RunMD 95.50 5.19 | Other 0.03 0.00 | ------------------------------ | Total 1840.13 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 3.04 0.17 | Build List 388.71 21.12 | --------------------------------- | Total 391.75 21.29 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 1053.07 57.23 | Exclude Masked 18.79 1.02 | Other 9.09 0.49 | --------------------------------- | Total 1080.95 58.74 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 21.12 1.15 | Grid Charges 34.72 1.89 | Scalar Sum 5.21 0.28 | Gradient Sum 47.61 2.59 | FFT 113.23 6.15 | --------------------------------- | Total 221.89 12.06 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 1 steps: | Elapsed(s) = 0.00 Per Step(ms) = 0.11 | ns/day = 1559.01 seconds/ns = 55.42 | | Average timings for all steps: | Elapsed(s) = 1840.14 Per Step(ms) = 92.01 | ns/day = 1.88 seconds/ns = 46003.49 | ----------------------------------------------------- | Setup CPU time: 0.08 seconds | NonSetup CPU time: 1840.13 seconds | Total CPU time: 1840.20 seconds 0.51 hours | Setup wall time: 0 seconds | NonSetup wall time: 1841 seconds | Total wall time: 1841 seconds 0.51 hours