------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 05/18/2008 at 19:09:11 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.1NLN_dspev |INPCRD: 1NLN_15A_solv_min.rst | PARM: 1NLN_15A_solv.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: MD of 1NLN const volume - QM atoms + 3 link atoms periodic &cntrl imin=0, irest=0, ntx=1, nstlim=4,dt=0.002, temp0=300.0,tempi=300.0, ntc=2, ntf=2, ntb=1, cut=8.0, ntt=1, ntpr=1, ifqnt=1 / &ewald use_pme=1 / &qmmm iqmatoms=1585,1586,1587,1588,1589,1590, 1591,1592,1593,1594,1595,1596,1597,1598,1599,1600,1601,1602, 1603,1604,1605,1606,1607,1608,1609,1610,1611,1612,1613,1614, 1615,1616,1617,1618, 3348,3349,3350,3351,3352,3353,3354,3355, 3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367, 3368,3369,3370,3371,3372,3373,3374,3375,3376, qm_theory='AM1', qmcharge=0, verbosity=0, qmshake=1, qmcut=8.0, qm_ewald=1, qm_pme=1, verbosity=0,writepdb=0,adjust_q=2, diag_routine=2, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI 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 = 37.070 | New format PARM file being parsed. | Version = 1.000 Date = 08/11/05 Time = 13:05:27 NATOM = 41778 NTYPES = 17 NBONH = 40054 MBONA = 1754 NTHETH = 3777 MTHETA = 2371 NPHIH = 7196 MPHIA = 4409 NHPARM = 0 NPARM = 0 NNB = 69799 NRES = 13026 NBONA = 1754 NTHETA = 2371 NPHIA = 4409 NUMBND = 42 NUMANG = 89 NPTRA = 39 NATYP = 30 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2216252 | Hollerith 263696 | Integer 1160650 | Max Pairs 3481500 | nblistReal 501336 | nblist Int 1871590 | Total 47705 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 = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, 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 = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 4, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 300.00000, tautp = 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 = 74.141 Box Y = 77.969 Box Z = 88.178 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 80 NFFT2 = 80 NFFT3 = 90 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 QMMM options: ifqnt = True nquant = 63 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 8.0000 qmshake = 1 lnk_atomic_no = 1 lnk_dis = 1.0900 qmmm_int = 1 qm_theory = AM1 verbosity = 0 qmqmdx = Analytical 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 diag_routine = 2 qm_ewald = 1 qm_pme = True kmaxqx = 5 kmaxqy = 5 kmaxqz = 5 ksqmaxq = 27 | MPI Timing options: | profile_mpi = 0 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 12795 | Atom division among processors: | 0 10446 20889 31332 41778 |QMMM: Running QMMM calculation in parallel mode on 4 threads. |QMMM: All atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 10445 ( 10445) |QMMM: Thread( 1): 10446-> 20890 ( 10445) |QMMM: Thread( 2): 20891-> 31335 ( 10445) |QMMM: Thread( 3): 31336-> 41778 ( 10443) |QMMM: Quantum atom + link atom division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 16 ( 16) |QMMM: Thread( 1): 17-> 32 ( 16) |QMMM: Thread( 2): 33-> 48 ( 16) |QMMM: Thread( 3): 49-> 66 ( 18) Sum of charges from parm topology file = -0.00000011 Forcing neutrality... | Running AMBER/MPI version on 4 nodes 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) = -0.750 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): 85280. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 85277. NUM_NOSHAKE = 0 CORRECTED RNDFP = 85277. | TOTAL # of degrees of freedom (RNDF) = 85277. --------------------------------------------------- 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 = 1932382 | TOTAL SIZE OF NONBOND LIST = 7346286 |QMMM: KVector division among threads: |QMMM: Start End Count |QMMM: Thread( 0): 1-> 78 ( 78) |QMMM: Thread( 1): 79-> 156 ( 78) |QMMM: Thread( 2): 157-> 234 ( 78) |QMMM: Thread( 3): 235-> 309 ( 75) QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 3 Link Coords Resp Charges QMMM: MM(typ) - QM(typ) X Y Z MM QM QMMM: 1583 N 1585 CT 0.111 2.087 -2.877 -0.348 -0.264 QMMM: 1619 CT 1617 N 0.523 4.461 3.808 -0.060 -0.416 QMMM: 3346 N 3348 CT 1.878 -1.357 3.594 -0.416 0.043 QMMM: ------------------------------------------------------------------------ -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- QMMM: SINGLET STATE CALCULATION QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 94 | QMMM: Parameter sets in use: | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990) | QMMM: *** Diagonalization Routine Information *** | QMMM: Pseudo diagonalizations are allowed. | QMMM: Auto diagonalization routine selection is disabled. | QMMM: Using dspev routine (diag_routine=2). | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- | QMMM: QM Atom Type Info : 1216 bytes | QMMM: QM RESP Charge Storage : 504 bytes | QMMM: QM Atom Number List : 264 bytes | QMMM: Link Atom Pairs : 120 bytes | QMMM: QM Atomic Number List : 264 bytes | QMMM: QM-MM Pair List : 166864 bytes | QMMM: QM Atom Mask : 83556 bytes | QMMM: QM Coordinate Arrays : 1338480 bytes | QMMM: Scaled MM Charge Array : 334224 bytes | QMMM: SCF Mulliken Charge Storage : 528 bytes | QMMM: QM Ewald Arrays : 252528 bytes | QMMM: QM Force Arrays : 1004256 bytes | QMMM: Density Matrix : 113568 bytes | QMMM: Density Matrix Copies : 114912 bytes | QMMM: Fock2 Density Matrix Workspace : 8448 bytes | QMMM: Fock Matrix : 113568 bytes | QMMM: Eigen Vector Storage : 225792 bytes | QMMM: QM-QM Elec Repulsion Integrals : 94512 bytes | QMMM: QM 2-Elec Repulsion Integrals : 539808 bytes | QMMM: 1-Electron Matrix : 113568 bytes | QMMM: _REAL_ parameter storage : 108744 bytes | QMMM: integer parameter storage : 2136 bytes | QMMM: QM-QM RIJ Eqns storage : 30072 bytes | QMMM: QM-MM RIJ Eqns storage : 929016 bytes | QMMM: _REAL_ Scratch arrays : 1974912 bytes | QMMM: Integer Scratch arrays : 557512 bytes | QMMM: --------------------------------------------------- | QMMM: Total Dynamic Memory Usage: 7.734 Mb QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1585 C -0.4720 1.4342 -2.2276 QMMM: 2 1586 H -1.4629 1.8810 -2.1467 QMMM: 3 1587 C -0.6276 0.0568 -2.8060 QMMM: 4 1588 H 0.3408 -0.4424 -2.8394 QMMM: 5 1589 H -1.2406 -0.5222 -2.1152 QMMM: 6 1590 C -1.2833 -0.0146 -4.1516 QMMM: 7 1591 H -2.3377 0.2568 -4.0994 QMMM: 8 1592 H -0.8088 0.6881 -4.8365 QMMM: 9 1593 C -1.1493 -1.3839 -4.7876 QMMM: 10 1594 H -1.5525 -1.3386 -5.7993 QMMM: 11 1595 H -0.0837 -1.5699 -4.9219 QMMM: 12 1596 N -1.6677 -2.4993 -4.0582 QMMM: 13 1597 H -1.1086 -2.7427 -3.2530 QMMM: 14 1598 C -2.7942 -3.2234 -4.3521 QMMM: 15 1599 N -3.5952 -2.9371 -5.4417 QMMM: 16 1600 H -3.3724 -2.1734 -6.0640 QMMM: 17 1601 H -4.4054 -3.5136 -5.6188 QMMM: 18 1602 N -3.1072 -4.2976 -3.5389 QMMM: 19 1603 H -2.5004 -4.4856 -2.7537 QMMM: 20 1604 H -3.9324 -4.8610 -3.6859 QMMM: 21 1605 C 0.0344 1.4060 -0.7793 QMMM: 22 1606 O -0.2727 0.4854 0.0257 QMMM: 23 1607 N 0.7707 2.5003 -0.3442 QMMM: 24 1608 H 1.0601 3.2134 -0.9983 QMMM: 25 1609 C 1.3612 2.5218 0.9566 QMMM: 26 1610 H 1.0008 1.6566 1.5131 QMMM: 27 1611 C 2.8871 2.3990 1.0078 QMMM: 28 1612 H 3.2241 3.2554 0.4237 QMMM: 29 1613 H 3.2196 2.6007 2.0260 QMMM: 30 1614 S 3.7860 0.9564 0.5209 QMMM: 31 1615 C 0.8791 3.7849 1.7760 QMMM: 32 1616 O 0.5148 4.8610 1.2308 QMMM: 33 1617 N 0.8384 3.6449 3.1583 QMMM: 34 1618 H 1.1236 2.7731 3.5811 QMMM: 35 3348 C 1.9600 -1.5251 2.5202 QMMM: 36 3349 H 1.6905 -0.6169 1.9811 QMMM: 37 3350 C 3.3755 -1.7855 2.0988 QMMM: 38 3351 H 3.6908 -2.7119 2.5788 QMMM: 39 3352 H 3.4261 -2.0334 1.0386 QMMM: 40 3353 S 4.4054 -0.3488 2.2044 QMMM: 41 3354 C 1.0046 -2.6213 2.1015 QMMM: 42 3355 O 0.8619 -3.6432 2.8251 QMMM: 43 3356 N 0.2941 -2.4008 0.9536 QMMM: 44 3357 H 0.4108 -1.5787 0.3786 QMMM: 45 3358 C -0.8151 -3.2410 0.5907 QMMM: 46 3359 H -0.7582 -4.1800 1.1413 QMMM: 47 3360 C -2.1686 -2.6105 0.9081 QMMM: 48 3361 H -2.2550 -1.6942 0.3241 QMMM: 49 3362 H -2.9354 -3.2939 0.5434 QMMM: 50 3363 C -2.3860 -2.3325 2.3406 QMMM: 51 3364 C -2.1265 -1.0616 2.8484 QMMM: 52 3365 H -1.7242 -0.3091 2.1864 QMMM: 53 3366 C -2.3774 -0.7639 4.1778 QMMM: 54 3367 H -2.1947 0.2342 4.5478 QMMM: 55 3368 C -2.8760 -1.7411 5.0265 QMMM: 56 3369 H -3.0722 -1.5144 6.0640 QMMM: 57 3370 C -3.1262 -3.0118 4.5326 QMMM: 58 3371 H -3.5078 -3.7765 5.1929 QMMM: 59 3372 C -2.8894 -3.3059 3.1988 QMMM: 60 3373 H -3.0875 -4.2991 2.8236 QMMM: 61 3374 C -0.7685 -3.7054 -0.9225 QMMM: 62 3375 O -1.4237 -4.7625 -1.1889 QMMM: 63 3376 O -0.0486 -3.0664 -1.7853 QMMM: 64 *H 0.1111 2.0868 -2.8773 QMMM: 65 *H 0.5232 4.4614 3.8079 QMMM: 66 *H 1.8784 -1.3568 3.5940 -------------------------------------------------------------------------------- 4. RESULTS --------------------------------------------------------------------------------