------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 10/10/2008 at 07:05:53 [-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 = -234217.5249 EKtot = 54561.1865 EPtot = -288778.7114 BOND = 1124.1853 ANGLE = 2911.7406 DIHED = 2246.1541 1-4 NB = 1334.3174 1-4 EEL = 15084.8396 VDWAALS = 36016.0524 EELEC = -347496.0008 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6269E-04 ------------------------------------------------------------------------------ NSTEP = 700 TIME(PS) = 2543.725 TEMP(K) = 299.42 PRESS = 0.0 Etot = -234218.1580 EKtot = 54984.8827 EPtot = -289203.0407 BOND = 1116.2858 ANGLE = 2998.6135 DIHED = 2201.0106 1-4 NB = 1300.3133 1-4 EEL = 15058.3182 VDWAALS = 36753.8140 EELEC = -348631.3962 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.8589E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 800 TIME(PS) = 2543.875 TEMP(K) = 299.78 PRESS = 0.0 Etot = -234218.5958 EKtot = 55051.9538 EPtot = -289270.5496 BOND = 1095.7118 ANGLE = 2914.4979 DIHED = 2243.1015 1-4 NB = 1316.4653 1-4 EEL = 15178.6680 VDWAALS = 36942.0875 EELEC = -348961.0817 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1789E-04 ------------------------------------------------------------------------------ NSTEP = 900 TIME(PS) = 2544.025 TEMP(K) = 298.58 PRESS = 0.0 Etot = -234216.0572 EKtot = 54831.5361 EPtot = -289047.5933 BOND = 1113.1289 ANGLE = 2927.4265 DIHED = 2273.3319 1-4 NB = 1300.1624 1-4 EEL = 15056.2663 VDWAALS = 36421.4878 EELEC = -348139.3971 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6092E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1000 TIME(PS) = 2544.175 TEMP(K) = 298.33 PRESS = 0.0 Etot = -234217.4772 EKtot = 54785.8374 EPtot = -289003.3146 BOND = 1111.4714 ANGLE = 2924.4856 DIHED = 2262.5783 1-4 NB = 1329.9984 1-4 EEL = 15119.8285 VDWAALS = 36707.3338 EELEC = -348459.0107 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4159E-04 ------------------------------------------------------------------------------ NSTEP = 1100 TIME(PS) = 2544.325 TEMP(K) = 297.62 PRESS = 0.0 Etot = -234217.8502 EKtot = 54654.6869 EPtot = -288872.5372 BOND = 1095.1463 ANGLE = 2955.5083 DIHED = 2267.8580 1-4 NB = 1327.1715 1-4 EEL = 15059.3246 VDWAALS = 36307.9654 EELEC = -347885.5114 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7718E-04 ------------------------------------------------------------------------------ NSTEP = 1200 TIME(PS) = 2544.475 TEMP(K) = 297.41 PRESS = 0.0 Etot = -234218.8013 EKtot = 54616.9197 EPtot = -288835.7211 BOND = 1094.4081 ANGLE = 2882.0596 DIHED = 2237.5926 1-4 NB = 1337.0428 1-4 EEL = 15132.3948 VDWAALS = 36262.4431 EELEC = -347781.6621 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1248E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1300 TIME(PS) = 2544.625 TEMP(K) = 298.83 PRESS = 0.0 Etot = -234221.5335 EKtot = 54876.5387 EPtot = -289098.0722 BOND = 1110.5299 ANGLE = 2888.9069 DIHED = 2243.2006 1-4 NB = 1275.5474 1-4 EEL = 15085.5690 VDWAALS = 36902.6236 EELEC = -348604.4495 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3887E-04 ------------------------------------------------------------------------------ NSTEP = 1400 TIME(PS) = 2544.775 TEMP(K) = 298.81 PRESS = 0.0 Etot = -234219.5616 EKtot = 54873.9069 EPtot = -289093.4685 BOND = 1109.7756 ANGLE = 2906.3201 DIHED = 2250.7295 1-4 NB = 1300.2081 1-4 EEL = 15072.2629 VDWAALS = 36906.1757 EELEC = -348638.9404 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4091E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1500 TIME(PS) = 2544.925 TEMP(K) = 298.90 PRESS = 0.0 Etot = -234218.8973 EKtot = 54889.5798 EPtot = -289108.4770 BOND = 1110.7974 ANGLE = 2987.1750 DIHED = 2222.5486 1-4 NB = 1320.4979 1-4 EEL = 15117.2033 VDWAALS = 36711.5334 EELEC = -348578.2326 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7548E-04 ------------------------------------------------------------------------------ NSTEP = 1600 TIME(PS) = 2545.075 TEMP(K) = 298.38 PRESS = 0.0 Etot = -234215.5446 EKtot = 54793.9224 EPtot = -289009.4670 BOND = 1132.7403 ANGLE = 2987.7216 DIHED = 2245.6961 1-4 NB = 1311.5852 1-4 EEL = 15085.2829 VDWAALS = 36587.4470 EELEC = -348359.9402 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5235E-04 ------------------------------------------------------------------------------ NSTEP = 1700 TIME(PS) = 2545.225 TEMP(K) = 297.07 PRESS = 0.0 Etot = -234218.4660 EKtot = 54554.8139 EPtot = -288773.2799 BOND = 1039.6999 ANGLE = 2990.2541 DIHED = 2261.5728 1-4 NB = 1328.4494 1-4 EEL = 15120.8432 VDWAALS = 36905.5958 EELEC = -348419.6951 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4710E-04 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 1800 TIME(PS) = 2545.375 TEMP(K) = 297.44 PRESS = 0.0 Etot = -234219.8777 EKtot = 54621.7688 EPtot = -288841.6464 BOND = 1107.9141 ANGLE = 2896.0314 DIHED = 2236.8386 1-4 NB = 1324.4401 1-4 EEL = 15135.2030 VDWAALS = 36692.6380 EELEC = -348234.7116 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1665E-04 ------------------------------------------------------------------------------ NSTEP = 1900 TIME(PS) = 2545.525 TEMP(K) = 299.25 PRESS = 0.0 Etot = -234220.8154 EKtot = 54954.2647 EPtot = -289175.0801 BOND = 1083.8976 ANGLE = 2945.5970 DIHED = 2268.7958 1-4 NB = 1318.5599 1-4 EEL = 15093.0171 VDWAALS = 36514.4494 EELEC = -348399.3969 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3755E-05 ------------------------------------------------------------------------------ check COM velocity, temp: 0.000000 0.00(Removed) NSTEP = 2000 TIME(PS) = 2545.675 TEMP(K) = 298.52 PRESS = 0.0 Etot = -234217.7823 EKtot = 54819.5697 EPtot = -289037.3520 BOND = 1081.3925 ANGLE = 2975.8407 DIHED = 2228.1735 1-4 NB = 1330.8877 1-4 EEL = 15181.7634 VDWAALS = 36500.9897 EELEC = -348336.3996 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2453E-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) = 298.38 PRESS = 0.0 Etot = -234218.3295 EKtot = 54795.0636 EPtot = -289013.3930 BOND = 1109.3511 ANGLE = 2941.2032 DIHED = 2247.2377 1-4 NB = 1315.7367 1-4 EEL = 15110.1060 VDWAALS = 36608.1197 EELEC = -348345.1474 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4074E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 2000 TIME(PS) = 2545.675 TEMP(K) = 0.76 PRESS = 0.0 Etot = 1.3679 EKtot = 138.9585 EPtot = 139.1821 BOND = 24.1800 ANGLE = 37.5308 DIHED = 19.9490 1-4 NB = 14.8742 1-4 EEL = 37.3730 VDWAALS = 241.6130 EELEC = 332.2434 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 1.0162 Ewald error estimate: 0.2399E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 9.78 4.93 | Nonbond 174.56 87.96 | Bond 0.04 0.02 | Angle 0.46 0.23 | Dihedral 1.92 0.97 | Shake 2.69 1.36 | RunMD 9.00 4.54 | Other 0.00 0.00 | ------------------------------ | Total 198.46 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 1.30 0.66 | Build List 15.62 7.87 | --------------------------------- | Total 16.92 8.53 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 75.83 38.21 | Exclude Masked 4.04 2.04 | Other 9.73 4.90 | --------------------------------- | Total 89.60 45.15 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 9.98 5.03 | Grid Charges 6.90 3.48 | Scalar Sum 2.69 1.35 | Gradient Sum 12.62 6.36 | FFT 35.83 18.06 | --------------------------------- | Total 68.02 34.27 | 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: 1.25 seconds | Master NonSetup CPU time: 199.99 seconds | Master Total CPU time: 201.24 seconds 0.06 hours | Master Setup wall time: 1 seconds | Master NonSetup wall time: 200 seconds | Master Total wall time: 201 seconds 0.06 hours