------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:42:27 | 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.cellulose_nvt.CPU | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: Typical Production MD NVT &cntrl ntx=5, irest=1, ntc=2, ntf=2, nstlim=20, ntpr=1, ntwx=0, ntwr=40, dt=0.002, cut=8., ntt=1, tautp=10.0, temp0=300.0, ntb=1, ntp=0, ioutfm=1, / &ewald nfft1=288, nfft2=128,nfft3=128, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 61.751 | New format PARM file being parsed. | Version = 1.000 Date = 05/13/05 Time = 14:32:09 | 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 = 408609 NTYPES = 8 NBONH = 360981 MBONA = 51840 NTHETH = 99576 MTHETA = 77652 NPHIH = 181764 MPHIA = 155196 NHPARM = 0 NPARM = 0 NNB = 976704 NRES = 110283 NBONA = 51840 NTHETA = 77652 NPHIA = 155196 NUMBND = 8 NUMANG = 14 NPTRA = 18 NATYP = 8 NPHB = 1 IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 57 27 27 | Direct force subcell size = 4.5479 4.6133 4.5742 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 40 iwrap = 0, ntwx = 0, 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 = 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 = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 0.00000, tautp = 10.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | 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 = 259.230 Box Y = 124.558 Box Z = 123.502 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 288 NFFT2 = 128 NFFT3 = 128 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 = 20.020 ps Number of triangulated 3-point waters found: 105855 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 10382407 | Integers 17339479 | Nonbonded Pairs Initial Allocation: 68247918 -------------------------------------------------------------------------------- 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) = 20.022 TEMP(K) = 300.39 PRESS = 0.0 Etot = -443331.6430 EKtot = 258123.4910 EPtot = -701455.1340 BOND = 20161.1310 ANGLE = 54279.6894 DIHED = 23615.3742 1-4 NB = 21934.3180 1-4 EEL = 742081.9778 VDWAALS = 97499.5980 EELEC = -1661027.2224 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2178E-03 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 20.024 TEMP(K) = 300.23 PRESS = 0.0 Etot = -443326.6490 EKtot = 257986.6208 EPtot = -701313.2698 BOND = 20184.9631 ANGLE = 54331.8278 DIHED = 23602.6464 1-4 NB = 21926.4544 1-4 EEL = 742086.0120 VDWAALS = 97527.7961 EELEC = -1660972.9696 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2181E-03 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 20.026 TEMP(K) = 300.06 PRESS = 0.0 Etot = -443322.1569 EKtot = 257843.1011 EPtot = -701165.2579 BOND = 20244.6794 ANGLE = 54343.8637 DIHED = 23594.4102 1-4 NB = 21914.0908 1-4 EEL = 742095.4811 VDWAALS = 97550.1958 EELEC = -1660907.9789 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2168E-03 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 20.028 TEMP(K) = 299.95 PRESS = 0.0 Etot = -443324.9225 EKtot = 257744.4482 EPtot = -701069.3707 BOND = 20302.0864 ANGLE = 54298.4140 DIHED = 23589.5719 1-4 NB = 21905.9680 1-4 EEL = 742107.8691 VDWAALS = 97574.5096 EELEC = -1660847.7896 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2204E-03 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 20.030 TEMP(K) = 299.85 PRESS = 0.0 Etot = -443328.7989 EKtot = 257665.3909 EPtot = -700994.1898 BOND = 20337.8081 ANGLE = 54243.4083 DIHED = 23586.1112 1-4 NB = 21910.0805 1-4 EEL = 742119.2344 VDWAALS = 97609.2220 EELEC = -1660800.0543 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2247E-03 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 20.032 TEMP(K) = 299.74 PRESS = 0.0 Etot = -443326.1284 EKtot = 257567.9591 EPtot = -700894.0875 BOND = 20359.0196 ANGLE = 54238.9941 DIHED = 23583.7198 1-4 NB = 21925.0292 1-4 EEL = 742125.5761 VDWAALS = 97643.6335 EELEC = -1660770.0598 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2297E-03 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 20.034 TEMP(K) = 299.66 PRESS = 0.0 Etot = -443318.0852 EKtot = 257499.8605 EPtot = -700817.9458 BOND = 20375.1633 ANGLE = 54263.1621 DIHED = 23583.4289 1-4 NB = 21942.6630 1-4 EEL = 742125.1553 VDWAALS = 97658.6136 EELEC = -1660766.1320 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2320E-03 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 20.036 TEMP(K) = 299.74 PRESS = 0.0 Etot = -443316.8396 EKtot = 257567.2613 EPtot = -700884.1009 BOND = 20381.1612 ANGLE = 54235.2184 DIHED = 23585.8216 1-4 NB = 21952.9963 1-4 EEL = 742120.0680 VDWAALS = 97639.6165 EELEC = -1660798.9829 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2372E-03 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 20.038 TEMP(K) = 300.00 PRESS = 0.0 Etot = -443324.4556 EKtot = 257788.5660 EPtot = -701113.0216 BOND = 20364.7400 ANGLE = 54138.7473 DIHED = 23590.6534 1-4 NB = 21954.7524 1-4 EEL = 742115.3874 VDWAALS = 97590.1157 EELEC = -1660867.4178 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2280E-03 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 20.040 TEMP(K) = 300.29 PRESS = 0.0 Etot = -443335.6526 EKtot = 258039.2109 EPtot = -701374.8635 BOND = 20320.1334 ANGLE = 54071.9672 DIHED = 23597.5154 1-4 NB = 21955.5098 1-4 EEL = 742116.2184 VDWAALS = 97523.4282 EELEC = -1660959.6359 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2282E-03 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 20.042 TEMP(K) = 300.44 PRESS = 0.0 Etot = -443337.0408 EKtot = 258168.4510 EPtot = -701505.4918 BOND = 20254.7390 ANGLE = 54147.6555 DIHED = 23606.0865 1-4 NB = 21961.2984 1-4 EEL = 742125.2567 VDWAALS = 97452.1220 EELEC = -1661052.6500 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2277E-03 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 20.044 TEMP(K) = 300.43 PRESS = 0.0 Etot = -443326.3797 EKtot = 258164.2341 EPtot = -701490.6138 BOND = 20188.8694 ANGLE = 54342.9990 DIHED = 23615.1609 1-4 NB = 21968.3776 1-4 EEL = 742142.7523 VDWAALS = 97377.5607 EELEC = -1661126.3337 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2226E-03 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 20.046 TEMP(K) = 300.43 PRESS = 0.0 Etot = -443319.6227 EKtot = 258158.1994 EPtot = -701477.8222 BOND = 20150.5287 ANGLE = 54489.9660 DIHED = 23622.0407 1-4 NB = 21968.3341 1-4 EEL = 742168.0029 VDWAALS = 97290.9889 EELEC = -1661167.6835 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2275E-03 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 20.048 TEMP(K) = 300.53 PRESS = 0.0 Etot = -443325.6006 EKtot = 258244.0728 EPtot = -701569.6734 BOND = 20162.8324 ANGLE = 54454.7871 DIHED = 23624.3030 1-4 NB = 21960.2319 1-4 EEL = 742200.0566 VDWAALS = 97192.4413 EELEC = -1661164.3257 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2314E-03 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 20.050 TEMP(K) = 300.66 PRESS = 0.0 Etot = -443334.4612 EKtot = 258359.6136 EPtot = -701694.0748 BOND = 20223.8949 ANGLE = 54287.7514 DIHED = 23621.9534 1-4 NB = 21951.0395 1-4 EEL = 742236.5802 VDWAALS = 97095.0032 EELEC = -1661110.2975 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2286E-03 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 20.052 TEMP(K) = 300.69 PRESS = 0.0 Etot = -443335.6074 EKtot = 258385.3172 EPtot = -701720.9247 BOND = 20294.9094 ANGLE = 54153.6112 DIHED = 23616.9706 1-4 NB = 21947.2504 1-4 EEL = 742272.3197 VDWAALS = 97008.4144 EELEC = -1661014.4003 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2271E-03 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 20.054 TEMP(K) = 300.59 PRESS = 0.0 Etot = -443327.6909 EKtot = 258300.9136 EPtot = -701628.6045 BOND = 20321.3292 ANGLE = 54144.6048 DIHED = 23611.4139 1-4 NB = 21952.5166 1-4 EEL = 742299.5201 VDWAALS = 96939.5300 EELEC = -1660897.5191 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2239E-03 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 20.056 TEMP(K) = 300.48 PRESS = 0.0 Etot = -443321.2933 EKtot = 258202.7867 EPtot = -701524.0800 BOND = 20284.7864 ANGLE = 54202.8289 DIHED = 23606.1457 1-4 NB = 21965.7886 1-4 EEL = 742311.0661 VDWAALS = 96888.8727 EELEC = -1660783.5683 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2279E-03 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 20.058 TEMP(K) = 300.45 PRESS = 0.0 Etot = -443325.1849 EKtot = 258174.3972 EPtot = -701499.5821 BOND = 20231.6617 ANGLE = 54229.2242 DIHED = 23601.3916 1-4 NB = 21975.0868 1-4 EEL = 742304.3587 VDWAALS = 96843.3904 EELEC = -1660684.6953 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2325E-03 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 20.060 TEMP(K) = 300.43 PRESS = 0.0 Etot = -443333.8534 EKtot = 258163.1189 EPtot = -701496.9723 BOND = 20227.2044 ANGLE = 54224.2138 DIHED = 23598.7964 1-4 NB = 21972.0858 1-4 EEL = 742282.9528 VDWAALS = 96797.7686 EELEC = -1660599.9940 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2383E-03 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 20.060 TEMP(K) = 300.25 PRESS = 0.0 Etot = -443327.1033 EKtot = 258007.3507 EPtot = -701334.4540 BOND = 20268.5821 ANGLE = 54256.1467 DIHED = 23602.6758 1-4 NB = 21947.1936 1-4 EEL = 742171.7923 VDWAALS = 97335.1411 EELEC = -1660915.9855 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2270E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 20.060 TEMP(K) = 0.32 PRESS = 0.0 Etot = 5.8649 EKtot = 273.2189 EPtot = 276.4278 BOND = 74.0324 ANGLE = 101.5863 DIHED = 13.3266 1-4 NB = 20.6053 1-4 EEL = 79.0951 VDWAALS = 293.6209 EELEC = 158.4443 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.5766E-05 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 54.08 89.65 | Bond 0.03 0.05 | Angle 0.42 0.70 | Dihedral 1.98 3.29 | Shake 0.46 0.76 | RunMD 3.35 5.55 | Other 0.00 0.00 | ------------------------------ | Total 60.32 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.12 0.21 | Build List 9.63 15.96 | --------------------------------- | Total 9.75 16.16 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 33.60 55.70 | Exclude Masked 0.88 1.46 | Other 0.33 0.55 | --------------------------------- | Total 34.82 57.71 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.75 1.25 | Grid Charges 1.24 2.06 | Scalar Sum 1.40 2.32 | Gradient Sum 1.85 3.06 | FFT 4.27 7.08 | --------------------------------- | Total 9.51 15.77 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 57.40 Per Step(ms) = 3021.10 | ns/day = 0.06 seconds/ns = 1510550.68 | | Average timings for all steps: | Elapsed(s) = 61.47 Per Step(ms) = 3073.64 | ns/day = 0.06 seconds/ns = 1536819.22 | ----------------------------------------------------- | Setup CPU time: 4.29 seconds | NonSetup CPU time: 60.32 seconds | Total CPU time: 64.62 seconds 0.02 hours | Setup wall time: 4 seconds | NonSetup wall time: 62 seconds | Total wall time: 66 seconds 0.02 hours