------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/13/2009 at 08:41:21 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: amoeba_jac.mdout | INPCRD: inpcrd | 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=1, irest=0, nstlim=10, ntpr=1, ntwr=10000, dt=0.001, vlimit=10.0, cut=8., jfastw=4, ntt=1, temp0=50.0,tempi=0.0, iamoeba=1, / &ewald nfft1=80,nfft2=80,nfft3=80, skinnb=2.,nbtell=0,order=5,ew_coeff=0.45, / &amoeba do_bond=1,do_ureyb=1,do_reg_angle=1,do_trig_angle=1, do_opbend=1,do_torsion=1,do_pi_torsion=1,do_strbend=1, do_torsion_torsion=1,do_amoeba_nonbond=1, dipole_scf_tol = 0.01,dipole_scf_iter_max=20, sor_coefficient=0.7,ee_damped_cut=4.5,ee_dsum_cut=6.7, beeman_integrator=1, / | New format inpcrd file being parsed. | Version = 1.000 Date = 12/20/05 Time = 16:49:26 | Conditional Compilation Defines Used: | AMOEBA | DIRFRC_COMTRANS | DIRFRC_EFS | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 31.115 | New format PARM file being parsed. | Version = 1.000 Date = 12/20/05 Time = 16:49:26 -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 23558 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 42280 NRES = 7182 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0 IFBOX = 1 NMXRS = 0 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 12 12 12 | Direct force subcell size = 5.1858 5.1858 5.1858 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- joint amber charmm General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, 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 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 10, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 10.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 50.00000, tempi = 0.00000, tautp = 1.00000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 62.230 Box Y = 62.230 Box Z = 62.230 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 80 NFFT2 = 80 NFFT3 = 80 Cutoff= 8.000 Tol =0.445E-07 Ewald Coefficient = 0.45000 Interpolation order = 5 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- joint amber charmm begin time read from input coords = 0.000 ps | Dynamic Memory, Types Used: | Reals 2149044 | Integers 1054874 | Nonbonded Pairs Initial Allocation: 5371224 -------------------------------------------------------------------------------- 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 = 0.8987E-11 at 2.875760 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.73 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 3.09 |--------------------------------------------------- | num_pairs_in_ee_cut, size_dipole_dipole_list = 1400443 1750553 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 1.20 PRESS = 0.0 Etot = -64536.8194 EKtot = 84.5980 EPtot = -64621.4174 BOND = 588.4488 ANGLE = 2903.4947 DIHED = 134.5373 1-4 NB = 1488.0638 1-4 EEL = 0.0000 VDWAALS = 30495.6386 EELEC = -71238.3022 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -28993.2983 Dipole convergence: rms = 0.786E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 15.89 PRESS = 0.0 Etot = -64467.8025 EKtot = 1115.6657 EPtot = -65583.4682 BOND = 663.2975 ANGLE = 2695.9485 DIHED = 132.2784 1-4 NB = 1469.4931 1-4 EEL = 0.0000 VDWAALS = 30955.4497 EELEC = -72043.7603 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -29456.1750 Dipole convergence: rms = 0.786E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 27.59 PRESS = 0.0 Etot = -64438.5378 EKtot = 1937.0261 EPtot = -66375.5638 BOND = 1414.6135 ANGLE = 2436.0536 DIHED = 127.9415 1-4 NB = 1438.0234 1-4 EEL = 0.0000 VDWAALS = 31738.1239 EELEC = -73336.4816 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30193.8380 Dipole convergence: rms = 0.786E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 32.93 PRESS = 0.0 Etot = -64425.2873 EKtot = 2312.5202 EPtot = -66737.8074 BOND = 2585.8317 ANGLE = 2260.9247 DIHED = 121.8077 1-4 NB = 1402.0861 1-4 EEL = 0.0000 VDWAALS = 32485.5977 EELEC = -74674.1928 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30919.8625 Dipole convergence: rms = 0.785E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 40.27 PRESS = 0.0 Etot = -64428.8415 EKtot = 2828.0478 EPtot = -67256.8893 BOND = 3231.7827 ANGLE = 2202.9996 DIHED = 114.2139 1-4 NB = 1369.8138 1-4 EEL = 0.0000 VDWAALS = 32856.1930 EELEC = -75660.1932 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -31371.6989 Dipole convergence: rms = 0.784E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 56.21 PRESS = 0.0 Etot = -64446.7957 EKtot = 3946.7461 EPtot = -68393.5419 BOND = 2740.3701 ANGLE = 2250.1672 DIHED = 105.5432 1-4 NB = 1346.8442 1-4 EEL = 0.0000 VDWAALS = 32683.1915 EELEC = -76095.7162 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -31423.9419 Dipole convergence: rms = 0.780E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 75.27 PRESS = 0.0 Etot = -64452.1860 EKtot = 5285.5539 EPtot = -69737.7398 BOND = 1559.3532 ANGLE = 2409.4181 DIHED = 96.2272 1-4 NB = 1335.4184 1-4 EEL = 0.0000 VDWAALS = 32056.4519 EELEC = -76052.4307 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -31142.1779 Dipole convergence: rms = 0.775E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 87.03 PRESS = 0.0 Etot = -64441.2432 EKtot = 6111.4200 EPtot = -70552.6632 BOND = 677.7969 ANGLE = 2663.8813 DIHED = 86.7218 1-4 NB = 1334.3539 1-4 EEL = 0.0000 VDWAALS = 31277.7753 EELEC = -75840.1425 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30753.0499 Dipole convergence: rms = 0.773E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 92.25 PRESS = 0.0 Etot = -64441.0934 EKtot = 6477.8448 EPtot = -70918.9382 BOND = 455.4427 ANGLE = 2905.3635 DIHED = 77.4740 1-4 NB = 1339.5944 1-4 EEL = 0.0000 VDWAALS = 30705.7662 EELEC = -75863.1639 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30539.4151 Dipole convergence: rms = 0.775E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 101.95 PRESS = 0.0 Etot = -64465.2085 EKtot = 7159.1609 EPtot = -71624.3694 BOND = 500.9375 ANGLE = 2993.0266 DIHED = 68.8732 1-4 NB = 1345.4648 1-4 EEL = 0.0000 VDWAALS = 30587.2858 EELEC = -76415.6825 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30704.2748 Dipole convergence: rms = 0.781E-02 iters = 5.00 ------------------------------------------------------------------------------ A V E R A G E S O V E R 10 S T E P S NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 53.06 PRESS = 0.0 Etot = -64454.3815 EKtot = 3725.8584 EPtot = -68180.2399 BOND = 1441.7875 ANGLE = 2572.1278 DIHED = 106.5618 1-4 NB = 1386.9156 1-4 EEL = 0.0000 VDWAALS = 31584.1474 EELEC = -74722.0066 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -30549.7732 Dipole convergence: rms = 0.781E-02 iters = 5.00 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 32.97 PRESS = 0.0 Etot = 30.4215 EKtot = 2315.3560 EPtot = 2303.4903 BOND = 999.4892 ANGLE = 283.4622 DIHED = 22.2712 1-4 NB = 55.8234 1-4 EEL = 0.0000 VDWAALS = 855.8419 EELEC = 1766.0541 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = 757.5092 Dipole convergence: rms = 0.476E-04 iters = 0.00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 52.59 97.59 | Bond 0.03 0.06 | Angle 0.04 0.07 | Dihedral 0.07 0.13 | Shake 0.00 0.00 | RunMD 1.16 2.15 | Other 0.00 0.00 | ------------------------------ | Total 53.89 | Amoeba Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.01 0.02 | Build List 0.46 0.85 | --------------------------------- | Total 0.47 0.87 | Amoeba Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 29.89 55.46 | Exclude Masked 0.92 1.71 | Other 1.06 1.97 | --------------------------------- | Total 31.87 59.14 | Amoeba Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 1.00 1.86 | Grid Charges 4.36 8.09 | Scalar Sum 1.01 1.87 | Gradient Sum 4.67 8.67 | FFT 9.35 17.35 | --------------------------------- | Total 20.39 37.84 | Setup CPU time: 1.32 seconds | NonSetup CPU time: 53.89 seconds | Total CPU time: 55.21 seconds 0.02 hours | Setup wall time: 2 seconds | NonSetup wall time: 54 seconds | Total wall time: 56 seconds 0.02 hours