------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | Run on 01/18/2017 at 17:17:47 | Executable path: sander | Working directory: /mnt/research/thermo/BuOHCycl/newgausfiles/testcode/10cutoffMultiQM/f3305/Freqonly | Hostname: dev-intel14 [-O]verwriting output File Assignments: | MDIN: qmtry.in | MDOUT: qmtry.out |INPCRD: c16.inpcrd | PARM: simbox.prmtop |RESTRT: restrt | 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: Testing tutorial on website for QMMM with Gaussian &cntrl imin=0,nstlim = 0, !do not run a minimization or MD run ntb=2, !constant pressure periodic boundary conditions ntf=2,ntc=2, cut=2.0, !1.0 ang classic bond cutoff ntp=1, ifqnt=1 !switch on QM/MM &end &qmmm qmmask=':16 <:3.0', qmcharge=0, qm_theory='EXTERN', qmcut=2.0, qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range interactions. &end &gau method = 'B3LYP', basis = '6-31G* Freq', &end -------------------------------------------------------------------------------- 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 = 17.743 | New format PARM file being parsed. | Version = 1.000 Date = 06/25/16 Time = 22:56:45 NATOM = 4530 NTYPES = 5 NBONH = 3020 MBONA = 1484 NTHETH = 7472 MTHETA = 1458 NPHIH = 11768 MPHIA = 1432 NHPARM = 0 NPARM = 0 NNB = 26200 NRES = 256 NBONA = 1484 NTHETA = 1458 NPHIA = 1432 NUMBND = 5 NUMANG = 8 NPTRA = 2 NATYP = 5 NPHB = 0 IFBOX = 1 NMXRS = 18 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 392885 | Hollerith 13848 | Integer 817952 | Max Pairs 96640 | nblistReal 54360 | nblist Int 1850319 | Total 14348 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 :16 <:3.0; matches 4530 atoms BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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 = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 2.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 0, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 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 = 35.486 Box Y = 35.544 Box Z = 35.532 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 2.000 Tol =0.100E-04 Ewald Coefficient = 1.50787 Interpolation order = 4 QMMM options: ifqnt = True nquant = 4530 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 2.0000 qmshake = 1 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 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- Cpptraj Generated Restart begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = -0.00002598 Forcing neutrality... | # of SOLUTE degrees of freedom (RNDFP): 10570. | # of SOLVENT degrees of freedom (RNDFS): 0. | QMSHAKE_NOSHAKEMASK_OVERLAP = 0 | NDFMIN = 10567. NUM_NOSHAKE = 0 CORRECTED RNDFP = 10567. | TOTAL # of degrees of freedom (RNDF) = 10567. --------------------------------------------------- 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 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 0 | TOTAL SIZE OF NONBOND LIST = 0 **************************************************** ERROR: QM region + cutoff larger than box dimension: QM-MM Cutoff = 2.0000 Coord Lower Upper Size Radius of largest sphere inside unit cell X -19.742 19.743 39.485 17.743 Y -19.771 19.763 39.534 17.743 Z -19.766 19.758 39.524 17.743 **************************************************** SANDER BOMB in subroutine QM_CHECK_PERIODIC QM region + cutoff larger than box cannot continue, need larger box.