------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/06/2008 at 10:08:48 [-O]verwriting output File Assignments: | MDIN: dtestinital.in | MDOUT: dtestinital.out |INPCRD: dmin2.rst | PARM: dimerwat.top |RESTRT: dtestinital.rst | REFC: dmin2.rst | MDVEL: mdvel | MDEN: mden | MDCRD: dtestinital.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 = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 10000, dt = 0.002 ntpr = 10, ntwx = 10, ntwr = 100 / solute fixed with weak restraint 1.0 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 = 300.00000, 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 1.00000 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) = 439.74 PRESS = 0.0 Etot = -11433.5222 EKtot = 3584.9367 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 = 149.91893822651309 NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = NaN PRESS = 0.0 Etot = NaN EKtot = NaN EPtot = NaN BOND = 25.8426 ANGLE = 56.4366 DIHED = 114.9663 1-4 NB = 50.9095 1-4 EEL = 0.0000 VDWAALS = 866.2008 EELEC = NaN EHBOND = 0.0000 RESTRAINT = 17705.2884 EAMBER (non-restraint) = NaN Ewald error estimate: NaN ------------------------------------------------------------------------------