------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 04/23/2006 at 11:15:14 [-O]verwriting output File Assignments: | MDIN: min_qmmm.in | MDOUT: min_qmmm.out |INPCRD: NMA.inpcrd | PARM: NMA.prmtop |RESTRT: min_qmmm.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Initial min of our structure QMMM &cntrl imin=1, maxcyc=500, ncyc=200, cut=8.0, ntb=1, ntc=2, ntf=2 ifqnt=1 / &qmmm qmmask=':1-2', 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 = 19.430 | New format PARM file being parsed. | Version = 1.000 Date = 04/22/06 Time = 14:22:14 NATOM = 4578 NTYPES = 9 NBONH = 4573 MBONA = 4 NTHETH = 14 MTHETA = 4 NPHIH = 22 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 6134 NRES = 1524 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 9 NUMANG = 10 NPTRA = 7 NATYP = 9 NPHB = 1 IFBOX = 1 NMXRS = 6 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 359215 | Hollerith 28994 | Integer 119793 | Max Pairs 1526000 | nblistReal 54936 | nblist Int 248585 | Total 10748 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals LOADING THE QUANTUM ATOMS AS GROUPS Mask :1-2; matches 12 atoms BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, 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 = 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 Energy minimization: maxcyc = 500, ncyc = 200, ntmin = 1 dx0 = 0.01000, drms = 0.00010 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 = 0 Box X = 38.861 Box Y = 40.343 Box Z = 40.136 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 40 NFFT2 = 40 NFFT3 = 40 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 QMMM options: ifqnt = True nquant = 12 qmgb = 0 qmcharge = 0 adjust_q = 2 spin = 1 qmcut = 8.0000 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 = 0.000 ps Number of triangulated 3-point waters found: 1522 Sum of charges from parm topology file = 0.00000000 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) = 0.000 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 = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 726780 | TOTAL SIZE OF NONBOND LIST = 726780 QMMM: Link Atom Information QMMM: ------------------------------------------------------------------------ QMMM: nlink = 0 QMMM: ------------------------------------------------------------------------ -------------------------------------------------------------------------------- 3.1 QM CALCULATION INFO -------------------------------------------------------------------------------- QMMM: SINGLET STATE CALCULATION QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15 | QMMM: Parameter sets in use: | QMMM: H : J.J.P.STEWART, JCC, 10, 209 (1989) | QMMM: C : J.J.P.STEWART, JCC, 10, 209 (1989) | QMMM: O : J.J.P.STEWART, JCC, 10, 209 (1989) | QMMM: N : J.J.P.STEWART, JCC, 10, 209 (1989) | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- | QMMM: QM Atom Type Info : 784 bytes | QMMM: QM RESP Charge Storage : 96 bytes | QMMM: QM Atom Number List : 48 bytes | QMMM: Link Atom Pairs : 0 bytes | QMMM: QM Atomic Number List : 48 bytes | QMMM: QM-MM Pair List : 18268 bytes | QMMM: QM Atom Mask : 9156 bytes | QMMM: QM Coordinate Arrays : 146784 bytes | QMMM: Scaled MM Charge Array : 36624 bytes | QMMM: SCF Mulliken Charge Storage : 96 bytes | QMMM: QM Ewald Arrays : 195480 bytes | QMMM: QM Force Arrays : 110160 bytes | QMMM: Density Matrix : 3024 bytes | QMMM: Density Matrix Copies : 6048 bytes | QMMM: Fock2 Density Matrix Workspace : 1536 bytes | QMMM: Fock Matrix : 3024 bytes | QMMM: Eigen Vector Storage : 5832 bytes | QMMM: QM-QM Elec Repulsion Integrals : 11616 bytes | QMMM: QM 2-Elec Repulsion Integrals : 10968 bytes | QMMM: 1-Electron Matrix : 3024 bytes | QMMM: _REAL_ parameter storage : 66816 bytes | QMMM: integer parameter storage : 360 bytes | QMMM: QM-QM RIJ Eqns storage : 3696 bytes | QMMM: QM-MM RIJ Eqns storage : 391248 bytes | QMMM: _REAL_ Scratch arrays : 110214 bytes | QMMM: Integer Scratch arrays : 54936 bytes | QMMM: --------------------------------------------------- | QMMM: Total Dynamic Memory Usage: 1.135 Mb QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: NO. ATOM X Y Z QMMM: 1 H 0.4488 -1.0024 2.0835 QMMM: 2 C -0.3075 -1.2981 1.3564 QMMM: 3 H -1.2609 -1.4500 1.8625 QMMM: 4 H 0.0056 -2.2244 0.8747 QMMM: 5 C -0.4541 -0.2045 0.3077 QMMM: 6 O -1.5684 0.1773 -0.0431 QMMM: 7 N 0.6761 0.3254 -0.1649 QMMM: 8 H 1.5684 -0.0115 0.1674 QMMM: 9 C 0.6713 1.3918 -1.1465 QMMM: 10 H -0.3518 1.7289 -1.3130 QMMM: 11 H 1.2725 2.2244 -0.7812 QMMM: 12 H 1.0906 1.0252 -2.0835 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.2769E+04 1.4992E+01 6.7012E+01 N 7 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 1569.6841 EEL = -14287.3591 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -51.4001 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.7032 EEL = -14012.9334 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2039 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.7004 EEL = -14012.9262 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2041 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.6984 EEL = -14012.9209 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2041 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.6965 EEL = -14012.9158 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2042 .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.6959 EEL = -14012.9143 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2041 .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.6953 EEL = -14012.9126 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2042 .... RESTARTED DUE TO LINMIN FAILURE ... ***** REPEATED LINMIN FAILURE ***** ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO ***** FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 314 -1.3185E+04 1.4042E+01 3.8399E+01 O 4108 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 881.6951 EEL = -14012.9122 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 PM3ESCF = -54.2042 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.01 ( 0.03% of Total) | Build the list 0.07 (54.69% of List ) | Other 0.06 (45.31% of List ) | List time 0.13 ( 0.32% of Nonbo) | Short_ene time 17.22 (98.38% of Direc) | Other 0.28 ( 1.62% of Direc) | Direct Ewald time 17.50 (43.77% of Ewald) | Adjust Ewald time 0.13 ( 0.34% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) | Fill Bspline coeffs 1.09 ( 4.90% of Recip) | Fill charge grid 3.80 (17.05% of Recip) | Scalar sum 3.54 (15.88% of Recip) | Grad sum 2.79 (12.50% of Recip) | FFT time 11.01 (49.36% of Recip) | Other 0.07 ( 0.31% of Recip) | Recip Ewald time 22.31 (55.82% of Ewald) | Virial junk 0.02 ( 0.05% of Ewald) | Other 0.00 ( 0.01% of Ewald) | Ewald time 39.97 (99.68% of Nonbo) | Nonbond force 40.10 (92.10% of Force) | QMMM ewald setup 0.00 ( 1.84% of QMMM ) | Other 0.00 (98.16% of QMMM ) | QMMM setup 0.00 ( 0.07% of QMMM ) | QMMM Ewald KTable 0.14 ( 3.96% of QMMM ) | QMMM list build 0.03 ( 0.96% of QMMM ) | QMMM prep coords 0.08 ( 2.48% of QMMM ) | QMMM RIJ Eqns Calc 0.22 ( 6.50% of QMMM ) | QMMM hcore QM-QM 0.11 (47.94% of QMMM ) | QMMM hcore QM-MM 0.12 (52.06% of QMMM ) | QMMM hcore calc 0.23 (16.02% of QMMM ) | QMMM Ewald Contrib 0.50 (86.34% of QMMM ) | Other 0.08 (13.66% of QMMM ) | QMMM fock build 0.58 (52.24% of QMMM ) | QMMM elec-energy cal 0.01 ( 0.83% of QMMM ) | QMMM full matrix dia 0.42 (38.33% of QMMM ) | QMMM pseudo matrix d 0.03 ( 2.78% of QMMM ) | QMMM density build 0.05 ( 4.52% of QMMM ) | Other 0.01 ( 1.30% of QMMM ) | QMMM scf 1.10 (75.33% of QMMM ) | QMMM ewald energy 0.12 ( 8.47% of QMMM ) | Other 0.00 ( 0.18% of QMMM ) | QMMM energy 1.47 (42.71% of QMMM ) | QMMM QM-QM force 0.17 ( 4.87% of QMMM ) | QMMM QM-MM force 0.44 (12.70% of QMMM ) | QMMM Ewald force 0.87 (25.42% of QMMM ) | QMMM Collate Forces 0.01 ( 0.21% of QMMM ) | Other 0.00 ( 0.12% of QMMM ) | QMMM 3.43 ( 7.88% of Force) | Other 0.01 ( 0.02% of Force) | Force time 43.54 (100.0% of Runmd) | Runmd Time 43.54 (99.21% of Total) | Other 0.33 ( 0.76% of Total) | Total time 43.89 (100.0% of ALL ) | Highest rstack allocated: 269948 | Highest istack allocated: 4578 | Job began at 11:15:14.976 on 04/23/2006 | Setup done at 11:15:15.059 on 04/23/2006 | Run done at 11:15:58.863 on 04/23/2006 | wallclock() was called 67334 times