------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/25/2009 at 12:31:33 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: FIX (active) full dynamics ( constraint dynamics: constant volume) &cntrl ntx = 7, irest = 1, ntpr = 100, ntwx = 0, ntwr = 0, ntf = 2, ntc = 2, tol = 0.000001, cut = 8.0, nstlim = 2000, dt = 0.00150, nscm = 250, ntt = 0, lastist = 4000000, lastrst = 5000000, / | WARNING: The sander lastist option is not needed and is ignored. | WARNING: The sander lastrst option is not needed and is ignored. | INFO: Axis order optimization will be used. | Conditional Compilation Defines Used: | MPI | SLOW_INDIRECTVEC | PUBFFT | Largest sphere to fit in unit cell has radius = 39.339 | INFO: Old style PARM file read | Duplicated 437 dihedrals | Duplicated 1846 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 90906 NTYPES = 19 NBONH = 87891 MBONA = 3077 NTHETH = 6433 MTHETA = 4178 NPHIH = 11305 MPHIA = 5519 NHPARM = 0 NPARM = 0 NNB = 145596 NRES = 28750 NBONA = 3077 NTHETA = 4178 NPHIA = 5519 NUMBND = 54 NUMANG = 126 NPTRA = 75 NATYP = 31 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 28 16 15 | Direct force subcell size = 5.0745 5.2086 5.2452 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- factor IX (ACTIVATED PROTEIN) 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 = 100, ntrx = 1, ntwr = 0 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 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 2000, nscm = 250, nrespa = 1 t = 0.00000, dt = 0.00150, 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 = 100 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 142.086 Box Y = 83.337 Box Z = 78.678 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 144 NFFT2 = 90 NFFT3 = 80 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 | PMEMD ewald parallel performance parameters: | block_fft = 0 | fft_blk_y_divisor = 2 | excl_recip = 0 | excl_master = 0 | atm_redist_freq = 320 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- factor IX (ACTIVATED PROTEIN) begin time read from input coords = 2542.675 ps Number of triangulated 3-point waters found: 28358 Sum of charges from parm topology file = 0.00031225 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 2903529 | Integers 2839092 | Nonbonded Pairs Initial Allocation: 2579457 | Running AMBER/MPI version on 8 nodes -------------------------------------------------------------------------------- 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 = 0.3338E-14 at 2.509280 | CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360 --------------------------------------------------- NSTEP = 100 TIME(PS) = 2542.825 TEMP(K) = 298.74 PRESS = 0.0 Etot = -234218.3473 EKtot = 54860.7625 EPtot = -289079.1098 BOND = 1103.0435 ANGLE = 2960.7695 DIHED = 2288.4338 1-4 NB = 1312.5562 1-4 EEL = 15093.0701 VDWAALS = 36866.8490 EELEC = -348703.8320 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6831E-04 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 2542.975 TEMP(K) = 297.76 PRESS = 0.0 Etot = -234218.3698 EKtot = 54681.6127 EPtot = -288899.9825 BOND = 1125.1379 ANGLE = 2961.9410 DIHED = 2244.2927 1-4 NB = 1316.1846 1-4 EEL = 15113.4142 VDWAALS = 36422.4567 EELEC = -348083.4097 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1472E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 300 TIME(PS) = 2543.125 TEMP(K) = 297.94 PRESS = 0.0 Etot = -234217.3995 EKtot = 54713.8798 EPtot = -288931.2793 BOND = 1136.6428 ANGLE = 2948.4126 DIHED = 2262.1544 1-4 NB = 1298.1550 1-4 EEL = 15134.1716 VDWAALS = 36703.9285 EELEC = -348414.7443 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1759E-04 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 2543.275 TEMP(K) = 298.80 PRESS = 0.0 Etot = -234217.5764 EKtot = 54870.9021 EPtot = -289088.4784 BOND = 1149.6321 ANGLE = 2884.9472 DIHED = 2223.7015 1-4 NB = 1308.3590 1-4 EEL = 15173.9831 VDWAALS = 36500.1800 EELEC = -348329.2813 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2372E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 500 TIME(PS) = 2543.425 TEMP(K) = 298.97 PRESS = 0.0 Etot = -234217.9535 EKtot = 54902.7462 EPtot = -289120.6997 BOND = 1145.4815 ANGLE = 2975.8144 DIHED = 2236.9885 1-4 NB = 1323.8331 1-4 EEL = 15106.6950 VDWAALS = 36536.3428 EELEC = -348445.8550 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3213E-04 ------------------------------------------------------------------------------ NSTEP = 600 TIME(PS) = 2543.575 TEMP(K) = 297.11 PRESS = 0.0 Etot = -234217.5256 EKtot = 54561.1864 EPtot = -288778.7120 BOND = 1124.1853 ANGLE = 2911.7406 DIHED = 2246.1541 1-4 NB = 1334.3174 1-4 EEL = 15084.8396 VDWAALS = 36016.0525 EELEC = -347496.0015 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6266E-04 ------------------------------------------------------------------------------ NSTEP = 700 TIME(PS) = 2543.725 TEMP(K) = 299.42 PRESS = 0.0 Etot = -234218.1563 EKtot = 54984.8832 EPtot = -289203.0395 BOND = 1116.2857 ANGLE = 2998.6134 DIHED = 2201.0107 1-4 NB = 1300.3133 1-4 EEL = 15058.3183 VDWAALS = 36753.8127 EELEC = -348631.3937 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8594E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 800 TIME(PS) = 2543.875 TEMP(K) = 299.78 PRESS = 0.0 Etot = -234218.5876 EKtot = 55051.9640 EPtot = -289270.5515 BOND = 1095.7114 ANGLE = 2914.4975 DIHED = 2243.1009 1-4 NB = 1316.4654 1-4 EEL = 15178.6695 VDWAALS = 36942.0831 EELEC = -348961.0794 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1844E-04 ------------------------------------------------------------------------------ NSTEP = 900 TIME(PS) = 2544.025 TEMP(K) = 298.58 PRESS = 0.0 Etot = -234216.0676 EKtot = 54831.0814 EPtot = -289047.1489 BOND = 1113.1312 ANGLE = 2927.4294 DIHED = 2273.3336 1-4 NB = 1300.1634 1-4 EEL = 15056.2583 VDWAALS = 36421.2781 EELEC = -348138.7430 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6048E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1000 TIME(PS) = 2544.175 TEMP(K) = 298.30 PRESS = 0.0 Etot = -234217.5641 EKtot = 54780.5436 EPtot = -288998.1077 BOND = 1111.4777 ANGLE = 2924.4924 DIHED = 2262.5603 1-4 NB = 1330.0118 1-4 EEL = 15119.8233 VDWAALS = 36706.5897 EELEC = -348453.0629 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4149E-04 ------------------------------------------------------------------------------ NSTEP = 1100 TIME(PS) = 2544.325 TEMP(K) = 297.40 PRESS = 0.0 Etot = -234217.6545 EKtot = 54613.7756 EPtot = -288831.4301 BOND = 1094.8186 ANGLE = 2955.6999 DIHED = 2267.8046 1-4 NB = 1327.1847 1-4 EEL = 15059.5012 VDWAALS = 36298.4475 EELEC = -347834.8867 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8346E-04 ------------------------------------------------------------------------------ NSTEP = 1200 TIME(PS) = 2544.475 TEMP(K) = 297.52 PRESS = 0.0 Etot = -234218.4683 EKtot = 54636.6265 EPtot = -288855.0948 BOND = 1095.2347 ANGLE = 2884.2823 DIHED = 2240.3010 1-4 NB = 1336.8241 1-4 EEL = 15132.4979 VDWAALS = 36199.6191 EELEC = -347743.8538 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1126E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1300 TIME(PS) = 2544.625 TEMP(K) = 299.88 PRESS = 0.0 Etot = -234220.9752 EKtot = 55069.6577 EPtot = -289290.6328 BOND = 1113.7048 ANGLE = 2897.6796 DIHED = 2251.3632 1-4 NB = 1273.6565 1-4 EEL = 15083.1261 VDWAALS = 37119.4591 EELEC = -349029.6221 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7247E-04 ------------------------------------------------------------------------------ NSTEP = 1400 TIME(PS) = 2544.775 TEMP(K) = 296.80 PRESS = 0.0 Etot = -234218.1824 EKtot = 54503.7991 EPtot = -288721.9815 BOND = 1105.9680 ANGLE = 2929.4514 DIHED = 2245.6212 1-4 NB = 1300.5759 1-4 EEL = 15083.3069 VDWAALS = 36582.2475 EELEC = -347969.1524 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6662E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1500 TIME(PS) = 2544.925 TEMP(K) = 299.31 PRESS = 0.0 Etot = -234220.1308 EKtot = 54965.9838 EPtot = -289186.1146 BOND = 1124.0054 ANGLE = 2956.1483 DIHED = 2244.5969 1-4 NB = 1297.5208 1-4 EEL = 15062.3454 VDWAALS = 36948.5904 EELEC = -348819.3219 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1397E-04 ------------------------------------------------------------------------------ NSTEP = 1600 TIME(PS) = 2545.075 TEMP(K) = 299.66 PRESS = 0.0 Etot = -234217.4282 EKtot = 55029.8283 EPtot = -289247.2566 BOND = 1127.5672 ANGLE = 3001.4723 DIHED = 2230.9204 1-4 NB = 1307.0504 1-4 EEL = 15082.8715 VDWAALS = 37118.8594 EELEC = -349115.9978 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5647E-04 ------------------------------------------------------------------------------ NSTEP = 1700 TIME(PS) = 2545.225 TEMP(K) = 298.12 PRESS = 0.0 Etot = -234219.7660 EKtot = 54746.1591 EPtot = -288965.9251 BOND = 1078.1372 ANGLE = 2932.9492 DIHED = 2228.8415 1-4 NB = 1320.5530 1-4 EEL = 15147.4896 VDWAALS = 36569.6283 EELEC = -348243.5238 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2566E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1800 TIME(PS) = 2545.375 TEMP(K) = 299.30 PRESS = 0.0 Etot = -234220.1760 EKtot = 54963.3839 EPtot = -289183.5600 BOND = 1124.7240 ANGLE = 2943.4797 DIHED = 2243.6940 1-4 NB = 1314.5326 1-4 EEL = 15124.8422 VDWAALS = 36689.9276 EELEC = -348624.7601 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2842E-04 ------------------------------------------------------------------------------ NSTEP = 1900 TIME(PS) = 2545.525 TEMP(K) = 298.26 PRESS = 0.0 Etot = -234218.7803 EKtot = 54772.8864 EPtot = -288991.6668 BOND = 1111.4489 ANGLE = 2949.7416 DIHED = 2229.6051 1-4 NB = 1334.6046 1-4 EEL = 15097.7428 VDWAALS = 36409.4909 EELEC = -348124.3007 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.9371E-05 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 2000 TIME(PS) = 2545.675 TEMP(K) = 298.79 PRESS = 0.0 Etot = -234218.9461 EKtot = 54870.3907 EPtot = -289089.3368 BOND = 1074.6951 ANGLE = 2925.0953 DIHED = 2219.8624 1-4 NB = 1322.7976 1-4 EEL = 15223.4016 VDWAALS = 36668.2394 EELEC = -348523.4284 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2667E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 2000 TIME(PS) = 2545.675 TEMP(K) = 298.52 PRESS = 0.0 Etot = -234218.4028 EKtot = 54820.6026 EPtot = -289039.0054 BOND = 1113.5517 ANGLE = 2939.2329 DIHED = 2244.2170 1-4 NB = 1313.7830 1-4 EEL = 15110.8184 VDWAALS = 36623.7041 EELEC = -348384.3125 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4099E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 2000 TIME(PS) = 2545.675 TEMP(K) = 0.88 PRESS = 0.0 Etot = 1.1297 EKtot = 162.1324 EPtot = 162.5463 BOND = 19.3461 ANGLE = 31.8120 DIHED = 19.5590 1-4 NB = 15.5034 1-4 EEL = 43.6532 VDWAALS = 283.1403 EELEC = 426.5117 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 0.9603 Ewald error estimate: 0.2514E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 9.75 4.88 | Nonbond 176.05 88.08 | Bond 0.03 0.02 | Angle 0.47 0.23 | Dihedral 1.91 0.96 | Shake 2.67 1.34 | RunMD 8.98 4.49 | Other 0.00 0.00 | ------------------------------ | Total 199.86 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 1.30 0.65 | Build List 15.74 7.87 | --------------------------------- | Total 17.04 8.53 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 75.83 37.94 | Exclude Masked 4.12 2.06 | Other 9.74 4.87 | --------------------------------- | Total 89.69 44.87 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 9.45 4.73 | Grid Charges 7.10 3.55 | Scalar Sum 2.68 1.34 | Gradient Sum 13.26 6.63 | FFT 36.82 18.42 | --------------------------------- | Total 69.30 34.68 | PME Load Balancing CPU Time, Average for All Tasks: | | Routine Sec % | ------------------------------------ | Atom Reassign 0.00 0.00 | Image Reassign 0.01 0.01 | FFT Reassign 0.00 0.00 | ------------------------------------ | Total 0.01 0.01 | Master Setup CPU time: 1.24 seconds | Master NonSetup CPU time: 200.62 seconds | Master Total CPU time: 201.86 seconds 0.06 hours | Master Setup wall time: 2 seconds | Master NonSetup wall time: 200 seconds | Master Total wall time: 202 seconds 0.06 hours