------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/13/2009 at 08:40:55 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.amoeba_gb1 | INPCRD: eq7.x | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short md, nve ensemble, verlet integrator &cntrl ntx=5, irest=1, nstlim=10, ntpr=1, ntwr=10000, ntave=250, dt=0.001, vlimit=10.0, cut=8., jfastw=4, ntt=0, temp0=300.0,tempi=300.0, gamma_ln=0.0, tautp=3.0, ntr=0, ntb=1, ntp=0, taup=2.0, ntwx=0, iamoeba=1, / &ewald nfft1=72,nfft2=72,nfft3=72, 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=0, / | INFO: Old style inpcrd file read | Conditional Compilation Defines Used: | AMOEBA | DIRFRC_COMTRANS | DIRFRC_EFS | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 20.225 | New format PARM file being parsed. | Version = 1.000 Date = 01/11/06 Time = 16:31:03 -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 9555 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 15910 NRES = 2956 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: 8 9 9 | Direct force subcell size = 5.0562 5.4882 5.3101 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- protein G, fragment B1 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 = 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 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 40.450 Box Y = 49.394 Box Z = 47.791 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 72 NFFT3 = 72 Cutoff= 8.000 Tol =0.445E-07 Ewald Coefficient = 0.45000 Interpolation order = 5 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- protein G, fragment B1 begin time read from input coords = 19.530 ps | Dynamic Memory, Types Used: | Reals 900964 | Integers 413610 | Nonbonded Pairs Initial Allocation: 2178540 -------------------------------------------------------------------------------- 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 = 583066 728832 NSTEP = 1 TIME(PS) = 19.531 TEMP(K) = 301.34 PRESS = 0.0 Etot = -19600.0373 EKtot = 8581.6435 EPtot = -28181.6808 BOND = 2769.4858 ANGLE = 1860.1922 DIHED = 1.6084 1-4 NB = 458.7986 1-4 EEL = 0.0000 VDWAALS = 12939.2955 EELEC = -33004.4673 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13206.5940 Dipole convergence: rms = 0.756E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 19.532 TEMP(K) = 303.24 PRESS = 0.0 Etot = -19608.9534 EKtot = 8635.8822 EPtot = -28244.8356 BOND = 2713.4868 ANGLE = 1869.2908 DIHED = 1.8476 1-4 NB = 459.5001 1-4 EEL = 0.0000 VDWAALS = 12937.2516 EELEC = -33016.3368 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13209.8755 Dipole convergence: rms = 0.753E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 19.533 TEMP(K) = 303.67 PRESS = 0.0 Etot = -19609.3742 EKtot = 8647.9321 EPtot = -28257.3063 BOND = 2718.2309 ANGLE = 1870.6077 DIHED = 2.1881 1-4 NB = 460.4874 1-4 EEL = 0.0000 VDWAALS = 12943.0591 EELEC = -33034.1676 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13217.7119 Dipole convergence: rms = 0.749E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 19.534 TEMP(K) = 302.23 PRESS = 0.0 Etot = -19601.3364 EKtot = 8607.1535 EPtot = -28208.4899 BOND = 2787.0285 ANGLE = 1867.6805 DIHED = 2.5480 1-4 NB = 461.6975 1-4 EEL = 0.0000 VDWAALS = 12956.3704 EELEC = -33055.2883 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13228.5266 Dipole convergence: rms = 0.746E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 19.535 TEMP(K) = 301.98 PRESS = 0.0 Etot = -19601.0594 EKtot = 8599.8853 EPtot = -28200.9447 BOND = 2816.8883 ANGLE = 1858.7151 DIHED = 2.8715 1-4 NB = 463.0206 1-4 EEL = 0.0000 VDWAALS = 12973.3654 EELEC = -33076.1590 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13239.6465 Dipole convergence: rms = 0.743E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 19.536 TEMP(K) = 303.33 PRESS = 0.0 Etot = -19604.0260 EKtot = 8638.4573 EPtot = -28242.4833 BOND = 2793.9039 ANGLE = 1843.6237 DIHED = 3.1396 1-4 NB = 464.3190 1-4 EEL = 0.0000 VDWAALS = 12988.7954 EELEC = -33089.9111 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13246.3537 Dipole convergence: rms = 0.741E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 19.537 TEMP(K) = 304.55 PRESS = 0.0 Etot = -19607.0326 EKtot = 8673.0643 EPtot = -28280.0970 BOND = 2757.9740 ANGLE = 1828.3559 DIHED = 3.3545 1-4 NB = 465.4397 1-4 EEL = 0.0000 VDWAALS = 12998.0531 EELEC = -33088.8928 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13244.3813 Dipole convergence: rms = 0.739E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 19.538 TEMP(K) = 304.12 PRESS = 0.0 Etot = -19606.7012 EKtot = 8660.7370 EPtot = -28267.4383 BOND = 2747.2977 ANGLE = 1821.8654 DIHED = 3.5099 1-4 NB = 466.2341 1-4 EEL = 0.0000 VDWAALS = 12998.1694 EELEC = -33070.7025 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13233.8123 Dipole convergence: rms = 0.738E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 19.539 TEMP(K) = 302.37 PRESS = 0.0 Etot = -19602.6161 EKtot = 8611.1064 EPtot = -28213.7225 BOND = 2760.8157 ANGLE = 1826.7052 DIHED = 3.5830 1-4 NB = 466.5747 1-4 EEL = 0.0000 VDWAALS = 12989.0035 EELEC = -33041.0860 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13219.3186 Dipole convergence: rms = 0.738E-02 iters = 5.00 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 19.540 TEMP(K) = 301.59 PRESS = 0.0 Etot = -19599.8099 EKtot = 8588.8978 EPtot = -28188.7077 BOND = 2749.8402 ANGLE = 1834.2521 DIHED = 3.5378 1-4 NB = 466.4434 1-4 EEL = 0.0000 VDWAALS = 12974.2927 EELEC = -33010.5299 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13206.5440 Dipole convergence: rms = 0.738E-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) = 19.540 TEMP(K) = 302.84 PRESS = 0.0 Etot = -19604.0946 EKtot = 8624.4760 EPtot = -28228.5706 BOND = 2761.4952 ANGLE = 1848.1289 DIHED = 2.8188 1-4 NB = 463.2515 1-4 EEL = 0.0000 VDWAALS = 12969.7656 EELEC = -33048.7541 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -13225.2765 Dipole convergence: rms = 0.744E-02 iters = 5.00 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 19.540 TEMP(K) = 1.04 PRESS = 0.0 Etot = 3.4748 EKtot = 29.5557 EPtot = 32.5947 BOND = 30.5964 ANGLE = 18.2909 DIHED = 0.6965 1-4 NB = 2.8296 1-4 EEL = 0.0000 VDWAALS = 22.9148 EELEC = 30.5374 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 1.6991 EPOLZ = 14.5911 Dipole convergence: rms = 0.625E-04 iters = 0.00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 24.10 99.10 | Bond 0.01 0.04 | Angle 0.05 0.21 | Dihedral 0.01 0.04 | Shake 0.00 0.00 | RunMD 0.15 0.62 | Other 0.00 0.00 | ------------------------------ | Total 24.32 | Amoeba Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.10 0.41 | --------------------------------- | Total 0.10 0.41 | Amoeba Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 11.66 47.94 | Exclude Masked 0.34 1.40 | Other 0.39 1.60 | --------------------------------- | Total 12.39 50.95 | Amoeba Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.31 1.27 | Grid Charges 2.18 8.96 | Scalar Sum 0.67 2.75 | Gradient Sum 1.97 8.10 | FFT 6.55 26.93 | --------------------------------- | Total 11.68 48.03 | Setup CPU time: 0.65 seconds | NonSetup CPU time: 24.32 seconds | Total CPU time: 24.97 seconds 0.01 hours | Setup wall time: 1 seconds | NonSetup wall time: 24 seconds | Total wall time: 25 seconds 0.01 hours