------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 03/13/2009 at 08:40:50 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: amoeba_wat1.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=300.0,tempi=0.0,tautp=1.0, ntp=0, iamoeba=1, / &ewald nfft1=24,nfft2=24,nfft3=24, skinnb=1.2,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=0, 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 = 18:01:24 | Conditional Compilation Defines Used: | AMOEBA | DIRFRC_COMTRANS | DIRFRC_EFS | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 9.322 | New format PARM file being parsed. | Version = 1.000 Date = 11/02/05 Time = 15:28:43 -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 648 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 648 NRES = 216 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 = 4.6608 4.6608 4.6608 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- water 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 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 18.643 Box Y = 18.643 Box Z = 18.643 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 -------------------------------------------------------------------------------- water box begin time read from input coords = 0.000 ps | Dynamic Memory, Types Used: | Reals 189205 | Integers 23117 | Nonbonded Pairs Initial Allocation: 115476 -------------------------------------------------------------------------------- 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 = 39766 49707 NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 287.20 PRESS = 0.0 Etot = -1366.7554 EKtot = 553.8941 EPtot = -1920.6495 BOND = 181.8195 ANGLE = 96.8105 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1033.4171 EELEC = -2257.0377 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -975.6588 Dipole convergence: rms = 0.971E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 291.07 PRESS = 0.0 Etot = -1367.1442 EKtot = 561.3534 EPtot = -1928.4976 BOND = 172.9513 ANGLE = 91.5774 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1031.4452 EELEC = -2251.7126 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -972.7590 Dipole convergence: rms = 0.969E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 295.74 PRESS = 0.0 Etot = -1366.9995 EKtot = 570.3540 EPtot = -1937.3535 BOND = 159.0392 ANGLE = 88.1546 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1024.9927 EELEC = -2241.8383 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -967.7016 Dipole convergence: rms = 0.963E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 294.16 PRESS = 0.0 Etot = -1366.8707 EKtot = 567.3192 EPtot = -1934.1899 BOND = 153.9442 ANGLE = 86.7918 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1014.6293 EELEC = -2228.5545 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -961.0006 Dipole convergence: rms = 0.955E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 288.43 PRESS = 0.0 Etot = -1366.8030 EKtot = 556.2647 EPtot = -1923.0677 BOND = 157.4625 ANGLE = 86.1295 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1002.7718 EELEC = -2215.1068 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -954.3248 Dipole convergence: rms = 0.947E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 284.69 PRESS = 0.0 Etot = -1366.6606 EKtot = 549.0406 EPtot = -1915.7013 BOND = 161.7125 ANGLE = 84.8406 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 992.7077 EELEC = -2205.2975 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -949.6646 Dipole convergence: rms = 0.941E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 288.95 PRESS = 0.0 Etot = -1367.5784 EKtot = 557.2608 EPtot = -1924.8393 BOND = 154.3937 ANGLE = 83.2451 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 987.1752 EELEC = -2201.5044 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -948.1488 Dipole convergence: rms = 0.939E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 292.63 PRESS = 0.0 Etot = -1367.0613 EKtot = 564.3613 EPtot = -1931.4226 BOND = 151.3718 ANGLE = 83.0319 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 987.0234 EELEC = -2203.4303 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -949.4194 Dipole convergence: rms = 0.940E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 286.57 PRESS = 0.0 Etot = -1366.4504 EKtot = 552.6839 EPtot = -1919.1343 BOND = 166.7490 ANGLE = 84.4338 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 990.8084 EELEC = -2208.9188 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -952.2067 Dipole convergence: rms = 0.942E-02 iters = 4.00 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 283.19 PRESS = 0.0 Etot = -1367.1835 EKtot = 546.1536 EPtot = -1913.3371 BOND = 176.4059 ANGLE = 85.1731 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 995.6633 EELEC = -2215.4243 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -955.1549 Dipole convergence: rms = 0.944E-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) = 289.26 PRESS = 0.0 Etot = -1366.9507 EKtot = 557.8686 EPtot = -1924.8193 BOND = 163.5850 ANGLE = 87.0188 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1006.0634 EELEC = -2222.8825 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -958.6039 Dipole convergence: rms = 0.951E-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) = 3.88 PRESS = 0.0 Etot = 0.3002 EKtot = 7.4853 EPtot = 7.5485 BOND = 9.9139 ANGLE = 4.0467 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 17.5315 EELEC = 19.6086 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = 9.6149 Dipole convergence: rms = 0.117E-03 iters = 0.00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.12 96.55 | Bond 0.01 0.86 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.00 0.00 | RunMD 0.03 2.59 | Other 0.00 0.00 | ------------------------------ | Total 1.16 | Amoeba Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.01 0.86 | --------------------------------- | Total 0.01 0.86 | Amoeba Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.73 62.93 | Exclude Masked 0.02 1.72 | Other 0.02 1.72 | --------------------------------- | Total 0.77 66.38 | Amoeba Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.07 6.03 | Scalar Sum 0.02 1.72 | Gradient Sum 0.07 6.03 | FFT 0.19 16.38 | --------------------------------- | Total 0.35 30.17 | Setup CPU time: 0.08 seconds | NonSetup CPU time: 1.16 seconds | Total CPU time: 1.24 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 1 seconds | Total wall time: 1 seconds 0.00 hours