------------------------------------------------------- Amber 16 SANDER 2016 ------------------------------------------------------- | Run on 02/27/2018 at 22:24:46 | Executable path: sander | Working directory: /home/Amber_DNA_QMMM/AAA_OPC/QMMM | Hostname: t7910 [-O]verwriting output File Assignments: | MDIN: AAA_salt_qmmm_orc_David4.in | MDOUT: AAA_salt_qmmm_orc_David4.out |INPCRD: inpcrd | PARM: AAA_salt.prmtop |RESTRT: AAA_salt_qmmm_orc_David4.rst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: cgataaatagc : Frame 1000 QMMM test &cntrl imin=0, ntb=1 cut=8.0, ntc=2, ntf=2, tempi = 310.15, temp0 = 310.15, ntt = 3, gamma_ln = 1.0, nstlim=0, dt=0.002, ntpr=1, ntwx=1,ifqnt=1 / &qmmm qmmask=':5-7,16-18|(:5-7,16-18<:9&:Na+)', qmcut=1.0, qmcharge=0, adjust_q=0, qm_theory='EXTERN', qmshake=0, qm_ewald=0, writepdb = 1 / &orc basis = 'sto-3g', method = 'hf', num_threads = 30 / -------------------------------------------------------------------------------- 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 = 23.124 | New format PARM file being parsed. | Version = 1.000 Date = 09/28/17 Time = 15:25:24 NATOM = 18490 NTYPES = 20 NBONH = 13552 MBONA = 4931 NTHETH = 597 MTHETA = 765 NPHIH = 1216 MPHIA = 1591 NHPARM = 0 NPARM = 0 NNB = 34968 NRES = 4515 NBONA = 4931 NTHETA = 765 NPHIA = 1591 NUMBND = 53 NUMANG = 103 NPTRA = 70 NATYP = 34 NPHB = 1 IFBOX = 2 NMXRS = 34 IFCAP = 0 NEXTRA = 4433 NCOPY = 0 | Memory Use Allocated | Real 1334892 | Hollerith 59987 | Integer 654067 | Max Pairs 7396000 | nblistReal 221880 | nblist Int 644835 | Total 46361 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals LOADING THE QUANTUM ATOMS AS GROUPS Mask :5-7,16-18|(:5-7,16-18<:9&:Na+); matches 232 atoms BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 1, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 0 ioutfm = 1, 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 = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 0, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 310.15000, tempi = 310.15000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Extra-points options: frameon = 1, chngmask= 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 56.641 Box Y = 56.641 Box Z = 56.641 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 60 NFFT2 = 60 NFFT3 = 60 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 QMMM options: ifqnt = True nquant = 232 qmgb = 0 qmcharge = 0 adjust_q = 0 spin = 1 qmcut = 1.0000 qmshake = 0 qmmm_int = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 lnk_method = 1 qm_theory = EXTERN verbosity = 0 qmqmdx = Analytical qm_ewald = 0 qm_pme = False | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 13552 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 13552 0 | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 4931 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 498 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 597 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 597 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 765 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 765 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1216 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1216 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1591 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1591 0 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- Cpptraj Generated Restart begin time read from input coords = 2020.000 ps Number of triangulated 3-point waters found: 4433 Sum of charges from parm topology file = 0.00002444 Forcing neutrality... | # of SOLUTE degrees of freedom (RNDFP): 41987. | # of SOLVENT degrees of freedom (RNDFS): 0. | QMSHAKE_NOSHAKEMASK_OVERLAP = 0 | NDFMIN = 41987. NUM_NOSHAKE = 0 CORRECTED RNDFP = 41987. | TOTAL # of degrees of freedom (RNDF) = 41987. --------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 5070482 | TOTAL SIZE OF NONBOND LIST = 5070482 **************************************************** ERROR: QM region + cutoff larger than box dimension: QM-MM Cutoff = 1.0000 Coord Lower Upper Size Radius of largest sphere inside unit cell X -36.389 29.076 65.464 23.124 Y -32.868 31.822 64.690 23.124 Z -23.825 23.562 47.387 23.124 **************************************************** SANDER BOMB in subroutine QM_CHECK_PERIODIC QM region + cutoff larger than box cannot continue, need larger box.