------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/13/2009 at 08:42:16 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: amoeba_formbox.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=7, irest=1, nstlim=10, ntpr=1, ntwr=1000,ntave=1000, nscm=1000,ntwx=0, dt=0.001, vlimit=10.0, cut=8.,maxcyc=50,ntmin=2,imin=0, ntt=1, temp0=298.0,tempi=0.0,tautp=1.0, ntp=0, iamoeba=1, / &ewald nfft1=24,nfft2=24,nfft3=24, skinnb=0.8,nbtell=0,order=5,ew_coeff=0.45, / &amoeba beeman_integrator=1, do_self=1,dipole_scf_tol = 0.01,dipole_scf_iter_max=30, sor_coefficient=0.7,ee_damped_cut=4.5,ee_dsum_cut=6.7, / | New format inpcrd file being parsed. | Version = 1.000 Date = 03/23/06 Time = 18:16:07 | Conditional Compilation Defines Used: | AMOEBA | DIRFRC_COMTRANS | DIRFRC_EFS | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 9.389 | New format PARM file being parsed. | Version = 1.000 Date = 12/19/05 Time = 17:52:21 -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 600 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 1500 NRES = 100 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: 4 4 4 | Direct force subcell size = 4.6945 4.6945 4.6945 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- formamide box 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 = 1, ntrx = 1, ntwr = 1000 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 = 298.00000, 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 = 18.778 Box Y = 18.778 Box Z = 18.778 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 24 NFFT2 = 24 NFFT3 = 24 Cutoff= 8.000 Tol =0.445E-07 Ewald Coefficient = 0.45000 Interpolation order = 5 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- formamide box begin time read from input coords = 0.000 ps | Dynamic Memory, Types Used: | Reals 185224 | Integers 38108 | Nonbonded Pairs Initial Allocation: 93798 -------------------------------------------------------------------------------- 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 = 32086 40107 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 312.50 PRESS = 0.0 Etot = -1273.4363 EKtot = 557.9738 EPtot = -1831.4101 BOND = 151.3336 ANGLE = 189.1582 DIHED = 22.3205 1-4 NB = 19.1968 1-4 EEL = 0.0000 VDWAALS = -97.2887 EELEC = -1838.1968 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -277.9337 Dipole convergence: rms = 0.839E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 308.81 PRESS = 0.0 Etot = -1273.0682 EKtot = 551.3751 EPtot = -1824.4433 BOND = 160.5444 ANGLE = 186.4807 DIHED = 22.1208 1-4 NB = 19.1702 1-4 EEL = 0.0000 VDWAALS = -99.6671 EELEC = -1836.6552 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -276.4372 Dipole convergence: rms = 0.836E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 302.74 PRESS = 0.0 Etot = -1273.3250 EKtot = 540.5496 EPtot = -1813.8746 BOND = 171.0614 ANGLE = 186.9175 DIHED = 21.8300 1-4 NB = 19.3727 1-4 EEL = 0.0000 VDWAALS = -102.6875 EELEC = -1835.3615 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -275.0072 Dipole convergence: rms = 0.833E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 304.04 PRESS = 0.0 Etot = -1273.7822 EKtot = 542.8617 EPtot = -1816.6439 BOND = 166.3480 ANGLE = 189.9608 DIHED = 21.4597 1-4 NB = 19.6772 1-4 EEL = 0.0000 VDWAALS = -105.9005 EELEC = -1834.3292 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -273.8598 Dipole convergence: rms = 0.831E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 309.22 PRESS = 0.0 Etot = -1273.6432 EKtot = 552.1098 EPtot = -1825.7531 BOND = 153.9700 ANGLE = 194.7554 DIHED = 21.0156 1-4 NB = 19.9501 1-4 EEL = 0.0000 VDWAALS = -108.8153 EELEC = -1833.5143 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -273.1147 Dipole convergence: rms = 0.832E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 310.14 PRESS = 0.0 Etot = -1273.4141 EKtot = 553.7490 EPtot = -1827.1630 BOND = 148.7273 ANGLE = 200.2576 DIHED = 20.5097 1-4 NB = 20.0943 1-4 EEL = 0.0000 VDWAALS = -111.0553 EELEC = -1832.9214 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -272.7751 Dipole convergence: rms = 0.833E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 304.71 PRESS = 0.0 Etot = -1273.1329 EKtot = 544.0673 EPtot = -1817.2002 BOND = 155.3579 ANGLE = 205.2732 DIHED = 19.9603 1-4 NB = 20.0616 1-4 EEL = 0.0000 VDWAALS = -112.4797 EELEC = -1832.6179 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -272.7556 Dipole convergence: rms = 0.836E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 297.83 PRESS = 0.0 Etot = -1273.0628 EKtot = 531.7857 EPtot = -1804.8486 BOND = 166.0142 ANGLE = 208.6816 DIHED = 19.3678 1-4 NB = 19.8552 1-4 EEL = 0.0000 VDWAALS = -113.1974 EELEC = -1832.6248 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -272.9451 Dipole convergence: rms = 0.839E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 296.89 PRESS = 0.0 Etot = -1273.3511 EKtot = 530.1015 EPtot = -1803.4526 BOND = 167.9908 ANGLE = 209.8587 DIHED = 18.7126 1-4 NB = 19.5318 1-4 EEL = 0.0000 VDWAALS = -113.4539 EELEC = -1832.8584 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -273.2342 Dipole convergence: rms = 0.841E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 301.96 PRESS = 0.0 Etot = -1273.5322 EKtot = 539.1545 EPtot = -1812.6866 BOND = 161.1398 ANGLE = 209.1340 DIHED = 17.9864 1-4 NB = 19.1922 1-4 EEL = 0.0000 VDWAALS = -113.4861 EELEC = -1833.1299 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -273.5231 Dipole convergence: rms = 0.842E-02 iters = 4.00 ------------------------------------------------------------------------------ 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) = 304.88 PRESS = 0.0 Etot = -1273.3748 EKtot = 544.3728 EPtot = -1817.7476 BOND = 160.2488 ANGLE = 198.0478 DIHED = 20.5283 1-4 NB = 19.6102 1-4 EEL = 0.0000 VDWAALS = -107.8032 EELEC = -1834.2209 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -274.1586 Dipole convergence: rms = 0.836E-02 iters = 4.00 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 4.97 PRESS = 0.0 Etot = 0.2283 EKtot = 8.8776 EPtot = 8.9280 BOND = 7.2370 ANGLE = 9.1952 DIHED = 1.4133 1-4 NB = 0.3493 1-4 EEL = 0.0000 VDWAALS = 5.7735 EELEC = 1.8275 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = 1.6720 Dipole convergence: rms = 0.367E-04 iters = 0.00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.02 96.23 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.01 0.94 | Shake 0.00 0.00 | RunMD 0.03 2.83 | Other 0.00 0.00 | ------------------------------ | Total 1.06 | Amoeba Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.01 0.94 | --------------------------------- | Total 0.01 0.94 | Amoeba Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.62 58.49 | Exclude Masked 0.03 2.83 | Other 0.02 1.89 | --------------------------------- | Total 0.67 63.21 | Amoeba Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.05 4.72 | Scalar Sum 0.03 2.83 | Gradient Sum 0.06 5.66 | FFT 0.21 19.81 | --------------------------------- | Total 0.35 33.02 | Setup CPU time: 0.10 seconds | NonSetup CPU time: 1.06 seconds | Total CPU time: 1.16 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 1 seconds | Total wall time: 1 seconds 0.00 hours