------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | Run on 05/07/2012 at 17:51:41 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: nma-spcfw-15.hf_sto-3g.mdout |INPCRD: nma-spcfw-15.restrt | PARM: nma-spcfw-15.prmtop |RESTRT: nma-spcfw-15.hf_sto-3g.restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: NMA in 15 Angstrom water shell QM/MM HF/STO-3G/SPC(Fw) NVE 2 steps at dt=0.5fs &cntrl imin = 0, ! do MD (no minimization) irest = 1, ! restart trajectory ntx = 5, ! read coordinates and velocities dt = 0.0005 ! 0.5fs time step cut = 999.9, ! non-bonded cutoff ntb = 0, ! periodic boundary conditions ntpr = 1, ! print every step) ntwx = 1, ! write coordinates every step ntwr = 2, ! write restart file at last step nstlim = 200, ! runfor 2 steps nscm = 0, ! do not remove COM motion jfastw = 4, ! do not use routines for fast triangulated water ioutfm = 1, ! NetCDF MDCRD. ifqnt = 1, ! do QMMM simulation / &qmmm qmmask = ':1-2', qm_theory = 'EXTERN', / &tc basis = '6-31G', method = 'PBE', charge = 0, spinmult = 1, mpi = 1, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 44.463 | New format PARM file being parsed. | Version = 1.000 Date = 08/22/10 Time = 18:49:10 NATOM = 1236 NTYPES = 9 NBONH = 823 MBONA = 4 NTHETH = 422 MTHETA = 4 NPHIH = 22 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 1678 NRES = 410 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 8 NUMANG = 11 NPTRA = 7 NATYP = 9 NPHB = 1 IFBOX = 0 NMXRS = 6 IFCAP = 1 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 61331 | Hollerith 4120 | Integer 48962 | Max Pairs 763230 | nblistReal 14832 | nblist Int 2428162 | Total 13268 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals LOADING THE QUANTUM ATOMS AS GROUPS Mask :1-2; matches 12 atoms -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 2 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.90000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 200, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00050, vlimit = 20.00000 Water cap: ivcap = 0, natcap = 12 fcap = 1.50000, cutcap = 15.00000 xcap = 2.46509, ycap = 2.08598, zcap = -0.00000 QMMM options: ifqnt = True nquant = 12 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 999.9000 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 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ACE begin time read from input coords = 20.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... QMMM: ADJUSTING CHARGES QMMM: ---------------------------------------------------------------------- QMMM: adjust_q = 2 QMMM: Uniformly adjusting the charge of MM atoms to conserve total charge. QMMM: qm_charge = 0 QMMM: QM atom RESP charge sum (inc MM link) = 0.000 QMMM: Adjusting each MM atom resp charge by = 0.000 QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 3708. | # of SOLVENT degrees of freedom (RNDFS): 0. | QMSHAKE_NOSHAKEMASK_OVERLAP = 0 | NDFMIN = 3708. NUM_NOSHAKE = 0 CORRECTED RNDFP = 3708. | TOTAL # of degrees of freedom (RNDF) = 3708. --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 761940 | TOTAL SIZE OF NONBOND LIST = 761940 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 0 QMMM: ------------------------------------------------------------------------ QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 H 4.8591 2.8057 2.0616 QMMM: 2 2 C 5.2450 1.9887 1.4384 QMMM: 3 3 H 4.5157 1.3897 0.8882 QMMM: 4 4 H 5.8660 1.4128 2.1408 QMMM: 5 5 C 6.0717 2.5983 0.3400 QMMM: 6 6 O 7.3106 2.6288 0.4621 QMMM: 7 7 N 5.4107 3.1011 -0.7462 QMMM: 8 8 H 4.3789 2.9860 -0.9672 QMMM: 9 9 C 6.1173 3.9877 -1.6735 QMMM: 10 10 H 6.9178 3.5319 -2.1627 QMMM: 11 11 H 5.3594 4.3079 -2.3711 QMMM: 12 12 H 6.4489 4.8962 -1.2384 -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- Constants for unit conversion taken from Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730 and using the thermochemical calorie (1 cal = 4.184 J): A_TO_BOHRS = 1.889726132873E+00 AU_TO_KCAL = 6.2750946943E+02 AU_TO_DEBYE = 2.54174623E+00 >>> Running QM calculation with TeraChem <<< | Searching for /home/c00jsw00/bin/TeraChem/terachem | Program terachem found! | &tc | basis = 6-31G | method = PBE | dftd = no | precision = mixed | executable = terachem | guess = scr/c0 | cis = no | threall = 1.00E-11 | convthre = 3.00E-05 | charge = 0 | spinmult = 1 | maxit = 100 | dftgrid = 1 | ngpus = 0 | cisnumstates = 1 | cistarget = 1 | mpi = 0 | ntpr = 1 | verbosity = 0 | dipole = F | use_template = F | / -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 1 TIME(PS) = 20.000 TEMP(K) = 326.05 PRESS = 0.0 Etot = -158141.8406 EKtot = 1201.2527 EPtot = -159343.0933 BOND = 426.5527 ANGLE = 266.5487 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1007.7218 EELEC = -5497.0884 EHBOND = 0.0000 RESTRAINT = 4.6666 EXTERNESCF= -155551.4948 EAMBER (non-restraint) = -159347.7599 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 20.001 TEMP(K) = 524.60 PRESS = 0.0 Etot = -158148.1509 EKtot = 1932.7620 EPtot = -160080.9129 BOND = 437.5698 ANGLE = 267.2499 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1007.2346 EELEC = -5490.8252 EHBOND = 0.0000 RESTRAINT = 4.6940 EXTERNESCF= -156306.8360 EAMBER (non-restraint) = -160085.6068 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 20.001 TEMP(K) = 901.17 PRESS = 0.0 Etot = -158158.1990 EKtot = 3320.1344 EPtot = -161478.3333 BOND = 543.1707 ANGLE = 276.0706 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1006.1917 EELEC = -5474.4952 EHBOND = 0.0000 RESTRAINT = 4.6899 EXTERNESCF= -157833.9611 EAMBER (non-restraint) = -161483.0233 ------------------------------------------------------------------------------ vlimit exceeded for step 3; vmax = 20.4984 NSTEP = 4 TIME(PS) = 20.002 TEMP(K) = 1412.46 PRESS = 0.0 Etot = -158174.9307 EKtot = 5203.8700 EPtot = -163378.8008 BOND = 882.1930 ANGLE = 307.1710 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1004.7581 EELEC = -5431.4921 EHBOND = 0.0000 RESTRAINT = 4.6560 EXTERNESCF= -160146.0869 EAMBER (non-restraint) = -163383.4568 ------------------------------------------------------------------------------ vlimit exceeded for step 4; vmax = 25.1250 NSTEP = 5 TIME(PS) = 20.002 TEMP(K) = 1989.37 PRESS = 0.0 Etot = -158306.4524 EKtot = 7329.3573 EPtot = -165635.8097 BOND = 1594.9570 ANGLE = 380.0823 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1003.1504 EELEC = -5337.5235 EHBOND = 0.0000 RESTRAINT = 4.5966 EXTERNESCF= -163281.0725 EAMBER (non-restraint) = -165640.4063 ------------------------------------------------------------------------------ vlimit exceeded for step 5; vmax = 27.7975 NSTEP = 6 TIME(PS) = 20.003 TEMP(K) = 2588.20 PRESS = 0.0 Etot = -158606.8849 EKtot = 9535.5779 EPtot = -168142.4629 BOND = 2733.0339 ANGLE = 517.3879 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1001.6066 EELEC = -5162.6794 EHBOND = 0.0000 RESTRAINT = 4.5181 EXTERNESCF= -167236.3300 EAMBER (non-restraint) = -168146.9810 ------------------------------------------------------------------------------ vlimit exceeded for step 6; vmax = 34.8471 NSTEP = 7 TIME(PS) = 20.003 TEMP(K) = 3226.99 PRESS = 0.0 Etot = -159017.7543 EKtot = 11889.0453 EPtot = -170906.7996 BOND = 4323.3785 ANGLE = 741.6366 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1000.3568 EELEC = -4874.9550 EHBOND = 0.0000 RESTRAINT = 4.4279 EXTERNESCF= -172101.6444 EAMBER (non-restraint) = -170911.2275 ------------------------------------------------------------------------------ vlimit exceeded for step 7; vmax = 41.4143 NSTEP = 8 TIME(PS) = 20.004 TEMP(K) = 3817.56 PRESS = 0.0 Etot = -159721.6314 EKtot = 14064.8766 EPtot = -173786.5080 BOND = 6472.6941 ANGLE = 1070.6179 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 999.5887 EELEC = -4441.8015 EHBOND = 0.0000 RESTRAINT = 4.3337 EXTERNESCF= -177891.9408 EAMBER (non-restraint) = -173790.8416 ------------------------------------------------------------------------------ vlimit exceeded for step 8; vmax = 80.3639 NSTEP = 9 TIME(PS) = 20.004 TEMP(K) = 4320.15 PRESS = 0.0 Etot = -160890.8280 EKtot = 15916.5440 EPtot = -176807.3720 BOND = 8878.1176 ANGLE = 1499.7892 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 999.1688 EELEC = -3756.3083 EHBOND = 0.0000 RESTRAINT = 4.2419 EXTERNESCF= -184432.3812 EAMBER (non-restraint) = -176811.6139 ------------------------------------------------------------------------------ vlimit exceeded for step 9; vmax = 153.7108 NSTEP = 10 TIME(PS) = 20.005 TEMP(K) = 4703.73 PRESS = 0.0 Etot = -163092.6217 EKtot = 17329.7236 EPtot = -180422.3453 BOND = 11002.0728 ANGLE = 2006.4052 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 998.2119 EELEC = -2979.7662 EHBOND = 0.0000 RESTRAINT = 4.1581 EXTERNESCF= -191453.4270 EAMBER (non-restraint) = -180426.5034 ------------------------------------------------------------------------------ vlimit exceeded for step 10; vmax = 43.7557 NSTEP = 11 TIME(PS) = 20.005 TEMP(K) = 5251.33 PRESS = 0.0 Etot = -160435.3247 EKtot = 19347.2487 EPtot = -179782.5734 BOND = 13555.5455 ANGLE = 2581.5672 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 999.2847 EELEC = -2308.9693 EHBOND = 0.0000 RESTRAINT = 4.0855 EXTERNESCF= -194614.0870 EAMBER (non-restraint) = -179786.6589 ------------------------------------------------------------------------------ vlimit exceeded for step 11; vmax = 32.7150 NSTEP = 12 TIME(PS) = 20.006 TEMP(K) = 5316.02 PRESS = 0.0 Etot = -159958.6929 EKtot = 19585.5614 EPtot = -179544.2543 BOND = 16857.6288 ANGLE = 3181.6733 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1002.8211 EELEC = -1277.1379 EHBOND = 0.0000 RESTRAINT = 4.0257 EXTERNESCF= -199313.2653 EAMBER (non-restraint) = -179548.2799 ------------------------------------------------------------------------------ vlimit exceeded for step 12; vmax = 106.2518 NSTEP = 13 TIME(PS) = 20.006 TEMP(K) = 5431.75 PRESS = 0.0 Etot = -161736.2756 EKtot = 20011.9450 EPtot = -181748.2206 BOND = 19166.1471 ANGLE = 3792.2668 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1006.8199 EELEC = -501.6086 EHBOND = 0.0000 RESTRAINT = 3.9786 EXTERNESCF= -205215.8245 EAMBER (non-restraint) = -181752.1992 ------------------------------------------------------------------------------ vlimit exceeded for step 13; vmax = 32.0400 NSTEP = 14 TIME(PS) = 20.007 TEMP(K) = 5454.52 PRESS = 0.0 Etot = -161762.8814 EKtot = 20095.8464 EPtot = -181858.7277 BOND = 21174.3543 ANGLE = 4374.3703 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1005.7173 EELEC = 332.9811 EHBOND = 0.0000 RESTRAINT = 3.9421 EXTERNESCF= -208750.0928 EAMBER (non-restraint) = -181862.6698 ------------------------------------------------------------------------------ vlimit exceeded for step 14; vmax = 161.8705 NSTEP = 15 TIME(PS) = 20.007 TEMP(K) = 5645.80 PRESS = 0.0 Etot = -164233.4659 EKtot = 20800.5604 EPtot = -185034.0263 BOND = 23304.5309 ANGLE = 4876.6060 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1008.8024 EELEC = 1106.0124 EHBOND = 0.0000 RESTRAINT = 3.9121 EXTERNESCF= -215333.8901 EAMBER (non-restraint) = -185037.9384 ------------------------------------------------------------------------------ vlimit exceeded for step 15; vmax = 39.7981 NSTEP = 16 TIME(PS) = 20.008 TEMP(K) = 6021.03 PRESS = 0.0 Etot = -160894.6176 EKtot = 22183.0105 EPtot = -183077.6281 BOND = 24062.9221 ANGLE = 5326.9862 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1002.3594 EELEC = 1850.3850 EHBOND = 0.0000 RESTRAINT = 3.8831 EXTERNESCF= -215324.1640 EAMBER (non-restraint) = -183081.5112 ------------------------------------------------------------------------------ SANDER BOMB in subroutine read_results (qm2_extern_tc_module) Error reading TeraChem output from file tc_job.dat ("FINAL ENERGY" or "dE/dX" or "MM / Point charge part" not found)