------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:23:07 | 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.noshake.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=1, ntf=1, tol=0.0000001, nstlim=10, ntt=0, ntpr=1, ntwr=10000, dt=0.001, / &ewald nfft1 = 72, nfft2 = 60, 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 = 1, 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 = 10, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 | 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 = 60 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 697030 | Integers 696344 | 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) = 210.40 PRESS = 0.0 Etot = -57482.1193 EKtot = 14380.1873 EPtot = -71862.3066 BOND = 452.1690 ANGLE = 1277.0334 DIHED = 968.3542 1-4 NB = 545.9440 1-4 EEL = 6666.3920 VDWAALS = 8109.3892 EELEC = -89881.5885 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3682E-04 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 510.052 TEMP(K) = 229.11 PRESS = 0.0 Etot = -57628.2594 EKtot = 15658.7449 EPtot = -73287.0042 BOND = 1090.4828 ANGLE = 1280.0548 DIHED = 969.1776 1-4 NB = 547.2444 1-4 EEL = 6662.8245 VDWAALS = 8104.7630 EELEC = -91941.5513 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2762E-04 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 510.053 TEMP(K) = 246.28 PRESS = 0.0 Etot = -57557.5211 EKtot = 16832.6014 EPtot = -74390.1225 BOND = 2988.3879 ANGLE = 1283.5010 DIHED = 971.2154 1-4 NB = 548.4280 1-4 EEL = 6659.0934 VDWAALS = 8097.8001 EELEC = -94938.5483 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5063E-04 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 510.054 TEMP(K) = 264.06 PRESS = 0.0 Etot = -57697.4473 EKtot = 18047.2497 EPtot = -75744.6970 BOND = 4429.6359 ANGLE = 1287.2073 DIHED = 974.2371 1-4 NB = 549.4167 1-4 EEL = 6654.7100 VDWAALS = 8094.5012 EELEC = -97734.4052 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7267E-04 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 510.055 TEMP(K) = 262.54 PRESS = 0.0 Etot = -57692.8765 EKtot = 17943.7235 EPtot = -75636.6000 BOND = 6999.0930 ANGLE = 1290.8097 DIHED = 977.8521 1-4 NB = 550.1208 1-4 EEL = 6649.1973 VDWAALS = 8099.8684 EELEC = -100203.5413 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5552E-04 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 510.056 TEMP(K) = 241.75 PRESS = 0.0 Etot = -57559.8493 EKtot = 16523.0712 EPtot = -74082.9205 BOND = 11203.6402 ANGLE = 1293.7471 DIHED = 981.5950 1-4 NB = 550.4484 1-4 EEL = 6642.3558 VDWAALS = 8115.7076 EELEC = -102870.4145 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6125E-04 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 510.057 TEMP(K) = 221.77 PRESS = 0.0 Etot = -57619.0510 EKtot = 15156.9711 EPtot = -72776.0221 BOND = 15289.4785 ANGLE = 1295.3315 DIHED = 985.0108 1-4 NB = 550.3240 1-4 EEL = 6634.4249 VDWAALS = 8139.9971 EELEC = -105670.5890 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7940E-04 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 510.058 TEMP(K) = 204.13 PRESS = 0.0 Etot = -57474.4418 EKtot = 13951.6122 EPtot = -71426.0539 BOND = 18438.3318 ANGLE = 1294.9323 DIHED = 987.7208 1-4 NB = 549.6959 1-4 EEL = 6626.0660 VDWAALS = 8168.0311 EELEC = -107490.8318 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8822E-04 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 510.059 TEMP(K) = 210.94 PRESS = 0.0 Etot = -57488.3596 EKtot = 14417.1208 EPtot = -71905.4804 BOND = 17610.2047 ANGLE = 1292.2549 DIHED = 989.4593 1-4 NB = 548.5419 1-4 EEL = 6618.1689 VDWAALS = 8195.2030 EELEC = -107159.3131 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.9858E-04 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 510.060 TEMP(K) = 239.12 PRESS = 0.0 Etot = -57654.1810 EKtot = 16342.8267 EPtot = -73997.0078 BOND = 13149.4936 ANGLE = 1287.5925 DIHED = 990.0880 1-4 NB = 546.8874 1-4 EEL = 6611.5622 VDWAALS = 8218.3045 EELEC = -104800.9359 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1083E-03 ------------------------------------------------------------------------------ A V E R A G E S O V E R 10 S T E P S NSTEP = 10 TIME(PS) = 510.060 TEMP(K) = 233.01 PRESS = 0.0 Etot = -57585.4106 EKtot = 15925.4109 EPtot = -73510.8215 BOND = 9165.0917 ANGLE = 1288.2465 DIHED = 979.4710 1-4 NB = 548.7051 1-4 EEL = 6642.4795 VDWAALS = 8134.3565 EELEC = -100269.1719 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6790E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 510.060 TEMP(K) = 20.25 PRESS = 0.0 Etot = 81.0133 EKtot = 1383.8483 EPtot = 1451.7913 BOND = 6490.2562 ANGLE = 6.0387 DIHED = 8.0216 1-4 NB = 1.4939 1-4 EEL = 18.2692 VDWAALS = 42.2806 EELEC = 6067.9579 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 21.1464 Ewald error estimate: 0.2495E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.34 86.83 | Bond 0.01 0.65 | Angle 0.00 0.00 | Dihedral 0.03 1.94 | Shake 0.00 0.00 | RunMD 0.16 10.59 | Other 0.00 0.00 | ------------------------------ | Total 1.55 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.19 | Build List 0.18 11.62 | --------------------------------- | Total 0.18 11.81 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.91 58.55 | Exclude Masked 0.02 1.29 | Other 0.01 0.52 | --------------------------------- | Total 0.93 60.36 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.02 1.10 | Grid Charges 0.02 1.61 | Scalar Sum 0.04 2.52 | Gradient Sum 0.03 2.26 | FFT 0.11 7.17 | --------------------------------- | Total 0.23 14.65 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 9 steps: | Elapsed(s) = 1.41 Per Step(ms) = 157.03 | ns/day = 0.55 seconds/ns = 157031.44 | | Average timings for all steps: | Elapsed(s) = 1.67 Per Step(ms) = 167.15 | ns/day = 0.52 seconds/ns = 167151.49 | ----------------------------------------------------- | Setup CPU time: 0.21 seconds | NonSetup CPU time: 1.55 seconds | Total CPU time: 1.76 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 2 seconds | Total wall time: 2 seconds 0.00 hours