------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 01/25/2008 at 14:04:05 [-O]verwriting output File Assignments: | MDIN: eqlb3.in | MDOUT: eqlb3.out |INPCRD: eqlb2.rst7 | PARM: box.prmtop |RESTRT: eqlb3.rst7 | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: eqlb3.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Equillibration Run &cntrl imin=0, irest=1, ntx=7, ntb = 2, ntp = 1 ntr=0, ntc=1, ntf=1, tempi=300.00, temp0=300.00, ntt=3, gamma_ln=1.0, nstlim = 5000, dt= 0.002, ntpr = 50, ntwx = 50, ntwr = 50, cut = 10 ifqnt = 1 / &qmmm iqmatoms= 1827, 1828, 1829, 1830, 1831, 1832, 3038, 3039, 3040, 3041, 3042, 3 qmcharge=0, spin=1, qmcharge=0, qmtheory=1, qmshake=1, qm_ewald=1, qm_pme=1 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 40.259 | New format PARM file being parsed. | Version = 1.000 Date = 11/15/07 Time = 10:34:47 NATOM = 63539 NTYPES = 21 NBONH = 59909 MBONA = 3755 NTHETH = 8010 MTHETA = 5182 NPHIH = 14873 MPHIA = 10835 NHPARM = 0 NPARM = 0 NNB = 114864 NRES = 19228 NBONA = 3755 NTHETA = 5182 NPHIA = 10835 NUMBND = 91 NUMANG = 197 NPTRA = 77 NATYP = 56 NPHB = 1 IFBOX = 1 NMXRS = 42 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 3134791 | Hollerith 400464 | Integer 1910273 | Max Pairs 36598464 | nblistReal 762468 | nblist Int 2395652 | Total 191794 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 50, ntrx = 1, ntwr = 50 iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 2, 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 = 0 Molecular dynamics: nstlim = 5000, 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 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 1.00000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 80.517 Box Y = 93.058 Box Z = 84.665 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 80 NFFT2 = 96 NFFT3 = 90 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 QMMM options: ifqnt = True nquant = 63 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 10.0000 qmshake = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 qmtheory = PM3 verbosity = 0 tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT]) scfconv = 0.100E-07 itrmax = 1000 printcharges = False peptide_corr = False qmqmrij_incore = True qmmmrij_incore = True qmqm_erep_incore = True pseudo_diag = True pseudo_diag_criteria = 0.0500 qm_ewald = 1 qm_pme = True kmaxqx = 5 kmaxqy = 5 kmaxqz = 5 ksqmaxq = 27 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 994.000 ps Number of triangulated 3-point waters found: 18809 Sum of charges from parm topology file = 0.00001980 Forcing neutrality... QMMM: ADJUSTING CHARGES QMMM: ---------------------------------------------------------------------- QMMM: adjust_q = 2 QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge. QMMM: qm_charge = 0 QMMM: QM atom RESP charge sum (inc MM link) = 0.510 QMMM: Adjusting each MM atom resp charge by = 0.000 QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- 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 = 0.3338E-14 at 2.509280 | CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 22927152 | TOTAL SIZE OF NONBOND LIST = 22927152 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 6 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 1825 CT 1827 CT -4.835 -2.508 4.581 0.007 -0.048 QMMM: 3036 CT 3038 CT -5.105 0.187 -0.601 0.007 -0.048 QMMM: 3048 CT 3050 CT -5.508 1.353 3.533 0.007 -0.048 QMMM: 7031 OS 7032 CT 0.269 4.474 2.819 -0.495 -0.007 QMMM: 7040 N* 7038 CT -0.240 5.231 -1.028 0.058 0.036 QMMM: 7092 n 7090 c3 2.363 1.637 -4.321 -0.067 0.378 QMMM: ------------------------------------------------------------------------ -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO --------------------------------------------------------------------------------