------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/05/2008 at 10:53:14 [-O]verwriting output File Assignments: | MDIN: dtestinital.in | MDOUT: dtestinitial.out |INPCRD: dmin2.rst | PARM: dimerwat.top |RESTRT: dtestinitial.rst | REFC: dmin2.rst | MDVEL: mdvel | MDEN: mden | MDCRD: dtestinitial.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: 20ps MD with res on solute &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 10000, dt = 0.002 ntpr = 10, ntwx = 10, ntwr = 100 / solute fixed with restraint 10.0 RES 1 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: SGIFFT getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 18.099 | New format PARM file being parsed. | Version = 1.000 Date = 06/02/08 Time = 14:25:10 NATOM = 4062 NTYPES = 9 NBONH = 3978 MBONA = 90 NTHETH = 234 MTHETA = 126 NPHIH = 426 MPHIA = 305 NHPARM = 0 NPARM = 0 NNB = 6268 NRES = 1295 NBONA = 90 NTHETA = 126 NPHIA = 305 NUMBND = 10 NUMANG = 18 NPTRA = 22 NATYP = 9 NPHB = 1 IFBOX = 1 NMXRS = 180 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 366559 | Hollerith 25669 | Integer 294613 | Max Pairs 2339712 | Max Rstack 269660 | Max Istack 20310 | Total 15440 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- MOL 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 = 10, ntrx = 1, ntwr = 100 iwrap = 0, ntwx = 10, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 10000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 41.123 Box Y = 39.757 Box Z = 36.199 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 48 NFFT2 = 40 NFFT3 = 36 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES MOL ----- READING GROUP 1; TITLE: solute fixed with weak restraint GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000 GRP 1 RES 1 TO 1 Number of atoms in this group = 180 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- MOL begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1294 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 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 = 0.2890E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8253E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 1029954 | TOTAL SIZE OF NONBOND LIST = 1029954 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -15018.4589 EKtot = 0.0000 EPtot = -15018.4589 BOND = 8.7900 ANGLE = 20.4093 DIHED = 112.9331 1-4 NB = 47.9624 1-4 EEL = 0.0000 VDWAALS = 2323.5071 EELEC = -17532.0608 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4187E-03 ------------------------------------------------------------------------------ vlimit exceeded for step 1 ; vmax = 191.82896720881251 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2345.1615 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 177128.1617 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 0.040 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2352.9619 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 1044724.5688 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 30 TIME(PS) = 0.060 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2498.3268 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 2635328.3150 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 40 TIME(PS) = 0.080 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2517.8073 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 4948939.4005 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2507.3594 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 7985557.8251 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 60 TIME(PS) = 0.120 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2424.9020 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 11745183.5890 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 70 TIME(PS) = 0.140 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2453.2739 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 16227816.6920 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 80 TIME(PS) = 0.160 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2529.0356 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 21433457.1343 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 90 TIME(PS) = 0.180 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2000.1883 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 27362104.9157 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2507.3003 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 34013760.0364 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 110 TIME(PS) = 0.220 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2356.8116 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 41388422.4962 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 120 TIME(PS) = 0.240 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2504.2400 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 49486092.2952 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------ NSTEP = 130 TIME(PS) = 0.260 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 8.4261 ANGLE = 20.8314 DIHED = 112.9519 1-4 NB = 48.0819 1-4 EEL = 0.0000 VDWAALS = 2506.4180 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 58306769.4335 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------