------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/13/2009 at 08:40:52 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: amoeba_wat2.out | 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=0, temp0=298.0,tempi=0.0,tautp=1.0,taup=1.0, ntp=0,ntb=1, iamoeba=1, / &ewald nfft1=30,nfft2=30,nfft3=30, skinnb=0.8,nbtell=0,order=5,ew_coeff=0.45, / &amoeba do_amoeba_nonbond=1,do_amoeba_valence=1,beeman_integrator=1, do_bond=1,do_ureyb=1,do_reg_angle=1,do_trig_angle=1, do_opbend=1,do_torsion=1,do_str_torsion=1,do_pi_torsion=1,do_strbend=1, do_torsion_torsion=1,do_induced=1,do_recip=1,do_direct=1,do_adjust=1, do_vdw=1,do_vdw_taper=1,do_vdw_longrange=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 = 18:13:24 | Conditional Compilation Defines Used: | AMOEBA | DIRFRC_COMTRANS | DIRFRC_EFS | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 9.063 | New format PARM file being parsed. | Version = 1.000 Date = 12/05/05 Time = 17:18:43 -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 843 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 843 NRES = 281 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: 5 5 5 | Direct force subcell size = 4.4398 4.4398 4.4398 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- octahedral waterbox 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 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 22.199 Box Y = 22.199 Box Z = 22.199 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 30 NFFT2 = 30 NFFT3 = 30 Cutoff= 8.000 Tol =0.445E-07 Ewald Coefficient = 0.45000 Interpolation order = 5 Setting ifbox to 3 for non-orthogonal unit cell -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- octahedral waterbox begin time read from input coords = 110.000 ps | Dynamic Memory, Types Used: | Reals 205804 | Integers 30072 | Nonbonded Pairs Initial Allocation: 131787 -------------------------------------------------------------------------------- 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 = 51782 64727 NSTEP = 1 TIME(PS) = 110.001 TEMP(K) = 296.07 PRESS = 0.0 Etot = -1782.1773 EKtot = 743.0870 EPtot = -2525.2643 BOND = 210.3178 ANGLE = 117.5250 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1266.3029 EELEC = -2888.2035 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1231.2064 Dipole convergence: rms = 0.893E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 110.002 TEMP(K) = 299.27 PRESS = 0.0 Etot = -1782.3921 EKtot = 751.1306 EPtot = -2533.5227 BOND = 195.9668 ANGLE = 122.3784 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1266.3646 EELEC = -2887.6342 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1230.5983 Dipole convergence: rms = 0.892E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 110.003 TEMP(K) = 295.79 PRESS = 0.0 Etot = -1781.4471 EKtot = 742.3902 EPtot = -2523.8373 BOND = 199.5017 ANGLE = 126.7644 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1269.6589 EELEC = -2888.5755 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1231.1869 Dipole convergence: rms = 0.894E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 110.004 TEMP(K) = 288.24 PRESS = 0.0 Etot = -1781.1236 EKtot = 723.4410 EPtot = -2504.5646 BOND = 215.2017 ANGLE = 128.0685 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1275.4225 EELEC = -2890.6090 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1232.6483 Dipole convergence: rms = 0.900E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 110.005 TEMP(K) = 289.04 PRESS = 0.0 Etot = -1782.0223 EKtot = 725.4432 EPtot = -2507.4654 BOND = 214.1492 ANGLE = 124.5505 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1281.4084 EELEC = -2893.0928 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1234.4807 Dipole convergence: rms = 0.905E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 110.006 TEMP(K) = 296.30 PRESS = 0.0 Etot = -1781.7729 EKtot = 743.6639 EPtot = -2525.4368 BOND = 202.0677 ANGLE = 118.0663 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1285.0353 EELEC = -2894.6872 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1235.9189 Dipole convergence: rms = 0.908E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 110.007 TEMP(K) = 298.50 PRESS = 0.0 Etot = -1781.3960 EKtot = 749.1840 EPtot = -2530.5800 BOND = 201.5461 ANGLE = 112.9048 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1284.9570 EELEC = -2894.0253 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1235.9627 Dipole convergence: rms = 0.909E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 110.008 TEMP(K) = 293.89 PRESS = 0.0 Etot = -1781.3181 EKtot = 737.6192 EPtot = -2518.9373 BOND = 212.2672 ANGLE = 112.1599 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1281.6003 EELEC = -2890.9064 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1234.0583 Dipole convergence: rms = 0.908E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 110.009 TEMP(K) = 289.08 PRESS = 0.0 Etot = -1781.7215 EKtot = 725.5327 EPtot = -2507.2542 BOND = 218.2131 ANGLE = 115.4032 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1276.4551 EELEC = -2886.5564 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1230.7692 Dipole convergence: rms = 0.903E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 110.010 TEMP(K) = 290.42 PRESS = 0.0 Etot = -1782.1192 EKtot = 728.9068 EPtot = -2511.0260 BOND = 208.8058 ANGLE = 119.2224 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1271.3722 EELEC = -2882.9375 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1227.4889 Dipole convergence: rms = 0.896E-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) = 110.010 TEMP(K) = 293.66 PRESS = 0.0 Etot = -1781.7490 EKtot = 737.0399 EPtot = -2518.7889 BOND = 207.8037 ANGLE = 119.7043 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1275.8577 EELEC = -2889.7228 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -1232.4318 Dipole convergence: rms = 0.901E-02 iters = 4.00 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 110.010 TEMP(K) = 3.93 PRESS = 0.0 Etot = 0.4003 EKtot = 9.8662 EPtot = 9.9580 BOND = 7.1533 ANGLE = 5.2892 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6.8653 EELEC = 3.4749 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = 2.5520 Dipole convergence: rms = 0.641E-04 iters = 0.00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.65 97.63 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.00 0.00 | RunMD 0.04 2.37 | Other 0.00 0.00 | ------------------------------ | Total 1.69 | Amoeba Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.01 0.59 | --------------------------------- | Total 0.01 0.59 | Amoeba Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.94 55.62 | Exclude Masked 0.01 0.59 | Other 0.03 1.78 | --------------------------------- | Total 0.98 57.99 | Amoeba Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.03 1.78 | Grid Charges 0.11 6.51 | Scalar Sum 0.04 2.37 | Gradient Sum 0.15 8.88 | FFT 0.33 19.53 | --------------------------------- | Total 0.66 39.05 | Setup CPU time: 0.08 seconds | NonSetup CPU time: 1.69 seconds | Total CPU time: 1.77 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 2 seconds | Total wall time: 2 seconds 0.00 hours