********>Bugfix 35: Author: Ross Walker Date: 04/17/2007 Programs: sander Description: When the printing of Mulliken charges is requested during QM/MM calculations the Mulliken charges that are printed are actually one step ahead of the energy that is printed. Thus on NSTEP=10 the Mulliken charges that are printed immediately after sander's energy data is printed are actually for the structure on step 11. This patch will fix this so that Mulliken charges are printed every ntpr steps and they correlate with the energy data output. This patch also updates the DFTB test cases to coincide with changes that were made by bugfix.18. Fix: Apply the following patches to src and test directories. Run this patch from the $AMBERHOME directory with "patch -p0". ------------------------------------------------------------------------------ *** src/sander/force.f 2006-04-03 16:35:55.000000000 -0700 --- src/sander/force.f 2007-04-17 13:07:36.000000000 -0700 *************** *** 368,374 **** qmmm_struct%mm_link_mask(j) = mm_link_mask( ncopy * j ) end do ! if(qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald > 0) & qm2_struct%scf_mchg = 0.0 nrg_scf = 0.0 --- 368,374 ---- qmmm_struct%mm_link_mask(j) = mm_link_mask( ncopy * j ) end do ! if(qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald > 0 .or. qmmm_nml%printcharges) & qm2_struct%scf_mchg = 0.0 nrg_scf = 0.0 *************** *** 442,448 **** # ifdef MPI ! if( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald > 0 ) then if(.not.qmmm_mpi%commqmmm_master) qm2_struct%scf_mchg = 0.0 --- 442,448 ---- # ifdef MPI ! if( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald > 0 .or. qmmm_nml%printcharges) then if(.not.qmmm_mpi%commqmmm_master) qm2_struct%scf_mchg = 0.0 *** src/sander/qm_mm.f 2006-04-03 16:35:55.000000000 -0700 --- src/sander/qm_mm.f 2007-04-17 12:44:42.000000000 -0700 *************** *** 81,87 **** !Locals _REAL_ , dimension(2,3) :: bxbnd ! _REAL_ :: mulliken_charge, total_mulliken_charge, total_energy _REAL_ :: alpb_beta integer :: ier=0 --- 81,87 ---- !Locals _REAL_ , dimension(2,3) :: bxbnd ! _REAL_ :: total_energy _REAL_ :: alpb_beta integer :: ier=0 *************** *** 411,440 **** !============================= ! Print Mulliken Charges !============================= ! if (qmmm_nml%printcharges .and. qmmm_mpi%master .and. qmmm_struct%ntpr_print) then ! call timer_start(TIME_QMMMMULLIK) ! total_mulliken_charge=0.0d0 ! write(6,'(" Atomic Charges:")') ! write(6,'(" Atom Element Mulliken Charge")') if ( qmmm_nml%qmtheory == DFTB .or. qm2_struct%calc_mchg_scf ) then ! do i=1,qmmm_struct%nquant_nlink ! !Mulliken charges have already been calculated and stored. ! mulliken_charge = scf_mchg(i) ! total_mulliken_charge=total_mulliken_charge+mulliken_charge ! write(6,'(" ",i5," ",A2," ",F14.3)') i, & ! element_sym(qmmm_struct%iqm_atomic_numbers(i)),mulliken_charge ! end do else do i=1,qmmm_struct%nquant_nlink !Need to calculate Mulliken charges here. ! call qm2_calc_mulliken(i,mulliken_charge) ! total_mulliken_charge=total_mulliken_charge+mulliken_charge ! write(6,'(" ",i5," ",A2," ",F14.3)') i, & ! element_sym(qmmm_struct%iqm_atomic_numbers(i)),mulliken_charge end do end if - write(6,'(" Total Mulliken Charge =",F12.3)') total_mulliken_charge - call timer_stop(TIME_QMMMMULLIK) end if !============================= ! End Print Mulliken Charges --- 411,430 ---- !============================= ! Print Mulliken Charges !============================= ! if (qmmm_nml%printcharges .and. qmmm_mpi%master) then ! !Calculate and store the mulliken charges on every step if we are ! !printing them. We only actually print on every ntpr steps but this ! !is done at the end of runmd so it is difficult to get a message in here ! !to calculate them only when needed. It isn't too harmful since for explicit ! !solvent PME or GB sims we calculate them on every step anyway. if ( qmmm_nml%qmtheory == DFTB .or. qm2_struct%calc_mchg_scf ) then ! !Mulliken charges have already been calculated and stored. else do i=1,qmmm_struct%nquant_nlink !Need to calculate Mulliken charges here. ! call qm2_calc_mulliken(i,scf_mchg(i)) end do end if end if !============================= ! End Print Mulliken Charges *** src/sander/qm_print_info.f 2006-04-03 16:35:55.000000000 -0700 --- src/sander/qm_print_info.f 2007-04-17 10:41:17.000000000 -0700 *************** *** 156,162 **** total_memory = total_memory + element_memory !SCF Mulliken Charge array ! if ( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald>0) then element_memory = size(qm2_struct%scf_mchg)*bytes_per_real write(6,'("| QMMM: SCF Mulliken Charge Storage : ",i12," bytes")') element_memory total_memory = total_memory + element_memory --- 156,163 ---- total_memory = total_memory + element_memory !SCF Mulliken Charge array ! if ( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald>0 & ! .or. qmmm_nml%printcharges) then element_memory = size(qm2_struct%scf_mchg)*bytes_per_real write(6,'("| QMMM: SCF Mulliken Charge Storage : ",i12," bytes")') element_memory total_memory = total_memory + element_memory *** src/sander/runmd.f 2007-04-17 13:25:44.000000000 -0700 --- src/sander/runmd.f 2007-04-17 12:52:05.000000000 -0700 *************** *** 8,14 **** subroutine runmd(xx,ix,ih,ipairs,x,winv,amass,f, & v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup,qpsander) ! use qmmm_module, only : qmmm_nml,qmmm_struct use constants, only : third, ten_to_minus3 use trace use stack --- 8,14 ---- subroutine runmd(xx,ix,ih,ipairs,x,winv,amass,f, & v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup,qpsander) ! use qmmm_module, only : qmmm_nml,qmmm_struct, qmmm_mpi, qm2_struct, element_sym use constants, only : third, ten_to_minus3 use trace use stack *************** *** 165,170 **** --- 165,174 ---- _REAL_ small data small/1.0d-7/ data nren/51/ + + !--- Variables for QMMM Muliken Charge Printing + _REAL_ :: total_mulliken_charge, mulliken_charge + !--- !--- VARIABLES FOR DIPOLE PRINTING --- integer prndipngrp *************** *** 2127,2132 **** --- 2131,2153 ---- if (lout) then if (facc /= 'A') rewind(7) call prntmd(nstep,nitp,nits,t,ener,onefac,7,.false.) + + !--- Print QMMM Muliken Charges if needed --- + if (qmmm_nml%ifqnt) then + if (qmmm_nml%printcharges .and. qmmm_mpi%master) then + total_mulliken_charge=0.0d0 + write(6,'(" Atomic Charges for Step",i8," :")') nstep + write(6,'(" Atom Element Mulliken Charge")') + do i=1,qmmm_struct%nquant_nlink + !Mulliken charges have already been calculated and stored. + mulliken_charge = qm2_struct%scf_mchg(i) + total_mulliken_charge=total_mulliken_charge+mulliken_charge + write(6,'(" ",i5," ",A2," ",F14.3)') i, & + element_sym(qmmm_struct%iqm_atomic_numbers(i)),mulliken_charge + end do + write(6,'(" Total Mulliken Charge =",F12.3)') total_mulliken_charge + end if + end if !--- BEGIN DIPOLE PRINTING CODE --- *** src/sander/runmin.f 2007-04-17 13:25:44.000000000 -0700 --- src/sander/runmin.f 2007-04-17 12:52:46.000000000 -0700 *************** *** 17,23 **** use fastwt use constants, only : zero, one, TEN_TO_MINUS5, TEN_TO_MINUS6 ! use qmmm_module, only : qmmm_nml, qmmm_struct #if defined( MPI ) use evb_data, only: evb_frc --- 17,23 ---- use fastwt use constants, only : zero, one, TEN_TO_MINUS5, TEN_TO_MINUS6 ! use qmmm_module, only : qmmm_nml, qmmm_struct, qmmm_mpi, element_sym, qm2_struct #if defined( MPI ) use evb_data, only: evb_frc *************** *** 81,86 **** --- 81,90 ---- logical qspatial _REAL_, dimension(:), allocatable :: frcti + !--- Variables for QMMM Muliken Charge Printing + _REAL_ :: total_mulliken_charge, mulliken_charge + !--- + integer maxlin,mxfcon,kstcyc ! comments on parameters are guesses by SRB Sep 2003 parameter ( maxlin = 10 ) ! maximum number of line searches ? *************** *** 249,254 **** --- 253,278 ---- if (lout) then call report_min_progress( n_force_calls, rms, fg, & ene(23), ih(m04) ) ! ih(m04) = atom names + + !--- Print QMMM Muliken Charges if needed --- + if (qmmm_nml%ifqnt) then + if (qmmm_nml%printcharges .and. qmmm_mpi%master) then + total_mulliken_charge=0.0d0 + write(6,'(" Atomic Charges for Step",i8," :")') n_force_calls + write(6,'(" Atom Element Mulliken Charge")') + do i=1,qmmm_struct%nquant_nlink + !Mulliken charges have already been calculated and stored. + mulliken_charge = qm2_struct%scf_mchg(i) + total_mulliken_charge=total_mulliken_charge+mulliken_charge + write(6,'(" ",i5," ",A2," ",F14.3)') i, & + element_sym(qmmm_struct%iqm_atomic_numbers(i)),mulliken_charge + end do + write(6,'(" Total Mulliken Charge =",F12.3)') total_mulliken_charge + end if + end if + + !--- BEGIN DIPOLE PRINTING CODE --- + end if !==================================================================== *** src/sander/sander.f 2007-04-17 13:25:44.000000000 -0700 --- src/sander/sander.f 2007-04-17 10:48:01.000000000 -0700 *************** *** 453,459 **** qmmm_mpi%nquant_nlink_start = 1 qmmm_mpi%nquant_nlink_end = qmmm_struct%nquant_nlink / ncopy !Now we know how many link atoms we can allocated the scf_mchg array... ! if ( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald>0) then !We need to allocate the memory for the mulliken charge array !Even if calc_mchg_scf is off for QM ewald since we will fill this !array with the muliken charges for the converged SCF. --- 453,460 ---- qmmm_mpi%nquant_nlink_start = 1 qmmm_mpi%nquant_nlink_end = qmmm_struct%nquant_nlink / ncopy !Now we know how many link atoms we can allocated the scf_mchg array... ! if ( qm2_struct%calc_mchg_scf .or. qmmm_nml%qm_ewald>0 .or. & ! qmmm_nml%printcharges) then !We need to allocate the memory for the mulliken charge array !Even if calc_mchg_scf is off for QM ewald since we will fill this !array with the muliken charges for the converged SCF. *** test/qmmm2/crambin_2/crambin_md_calc_mulliken.out.save 2006-04-03 18:14:07.000000000 -0700 --- test/qmmm2/crambin_2/crambin_md_calc_mulliken.out.save 2007-04-17 13:23:08.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/09/2006 at 14:08:48 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 13:17:45 [-O]verwriting output File Assignments: *************** *** 173,178 **** --- 173,179 ---- | QMMM: QM Atom Mask : 1284 bytes | QMMM: QM Coordinate Arrays : 21120 bytes | QMMM: Scaled MM Charge Array : 5136 bytes + | QMMM: SCF Mulliken Charge Storage : 192 bytes | QMMM: QM Force Arrays : 15984 bytes | QMMM: Density Matrix : 14640 bytes | QMMM: Density Matrix Copies : 29280 bytes *************** *** 240,246 **** AM1ESCF= -48.8684 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.553 2 H 0.260 --- 241,283 ---- AM1ESCF= -48.8684 ------------------------------------------------------------------------------ ! Atomic Charges for Step 1 : ! Atom Element Mulliken Charge ! 1 N -0.555 ! 2 H 0.262 ! 3 C 0.006 ! 4 H 0.111 ! 5 C -0.243 ! 6 H 0.170 ! 7 H 0.079 ! 8 S -0.063 ! 9 C 0.183 ! 10 O -0.282 ! 11 N -0.537 ! 12 H 0.210 ! 13 C 0.023 ! 14 H 0.125 ! 15 C -0.245 ! 16 H 0.092 ! 17 H 0.109 ! 18 S -0.042 ! 19 C 0.193 ! 20 O -0.256 ! 21 H 0.314 ! 22 H 0.042 ! 23 H 0.353 ! 24 H -0.049 ! Total Mulliken Charge = 0.000 ! ! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 2.90 PRESS = 0.0 ! Etot = -1017.4918 EKtot = 5.5315 EPtot = -1023.0233 ! BOND = 17.0352 ANGLE = 75.4380 DIHED = 182.2628 ! 1-4 NB = 179.2692 1-4 EEL = 1439.5683 VDWAALS = -248.1788 ! EELEC = -2618.2304 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -50.1877 ! ------------------------------------------------------------------------------ ! ! Atomic Charges for Step 2 : Atom Element Mulliken Charge 1 N -0.553 2 H 0.260 *************** *** 268,282 **** 24 H -0.048 Total Mulliken Charge = 0.000 ! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 2.90 PRESS = 0.0 ! Etot = -1017.4918 EKtot = 5.5315 EPtot = -1023.0233 ! BOND = 17.0352 ANGLE = 75.4380 DIHED = 182.2628 ! 1-4 NB = 179.2692 1-4 EEL = 1439.5683 VDWAALS = -248.1788 ! EELEC = -2618.2304 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -50.1877 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.548 2 H 0.258 --- 305,319 ---- 24 H -0.048 Total Mulliken Charge = 0.000 ! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 9.17 PRESS = 0.0 ! Etot = -1019.2203 EKtot = 17.4914 EPtot = -1036.7117 ! BOND = 14.3681 ANGLE = 73.9226 DIHED = 181.9559 ! 1-4 NB = 178.6660 1-4 EEL = 1437.6841 VDWAALS = -250.1922 ! EELEC = -2619.8474 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -53.2687 ------------------------------------------------------------------------------ ! Atomic Charges for Step 3 : Atom Element Mulliken Charge 1 N -0.548 2 H 0.258 *************** *** 304,318 **** 24 H -0.045 Total Mulliken Charge = 0.000 ! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 9.17 PRESS = 0.0 ! Etot = -1019.2203 EKtot = 17.4915 EPtot = -1036.7117 ! BOND = 14.3681 ANGLE = 73.9226 DIHED = 181.9559 ! 1-4 NB = 178.6660 1-4 EEL = 1437.6841 VDWAALS = -250.1922 ! EELEC = -2619.8474 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -53.2687 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.541 2 H 0.254 --- 341,355 ---- 24 H -0.045 Total Mulliken Charge = 0.000 ! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 15.80 PRESS = 0.0 ! Etot = -1019.0780 EKtot = 30.1354 EPtot = -1049.2134 ! BOND = 13.5333 ANGLE = 72.0719 DIHED = 181.5124 ! 1-4 NB = 177.7970 1-4 EEL = 1434.8225 VDWAALS = -253.1910 ! EELEC = -2619.9691 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -55.7905 ------------------------------------------------------------------------------ ! Atomic Charges for Step 4 : Atom Element Mulliken Charge 1 N -0.541 2 H 0.254 *************** *** 340,354 **** 24 H -0.041 Total Mulliken Charge = 0.000 ! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 15.80 PRESS = 0.0 ! Etot = -1019.0780 EKtot = 30.1354 EPtot = -1049.2134 ! BOND = 13.5333 ANGLE = 72.0719 DIHED = 181.5124 ! 1-4 NB = 177.7970 1-4 EEL = 1434.8225 VDWAALS = -253.1910 ! EELEC = -2619.9691 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -55.7905 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.534 2 H 0.253 --- 377,391 ---- 24 H -0.041 Total Mulliken Charge = 0.000 ! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 21.27 PRESS = 0.0 ! Etot = -1019.3375 EKtot = 40.5823 EPtot = -1059.9199 ! BOND = 15.2381 ANGLE = 70.5916 DIHED = 181.0117 ! 1-4 NB = 176.7995 1-4 EEL = 1431.2552 VDWAALS = -256.9021 ! EELEC = -2620.9136 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.0003 ------------------------------------------------------------------------------ ! Atomic Charges for Step 5 : Atom Element Mulliken Charge 1 N -0.534 2 H 0.253 *************** *** 376,390 **** 24 H -0.037 Total Mulliken Charge = 0.000 ! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 21.27 PRESS = 0.0 ! Etot = -1019.3375 EKtot = 40.5823 EPtot = -1059.9199 ! BOND = 15.2381 ANGLE = 70.5916 DIHED = 181.0117 ! 1-4 NB = 176.7995 1-4 EEL = 1431.2552 VDWAALS = -256.9021 ! EELEC = -2620.9136 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.0003 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.528 2 H 0.253 --- 413,427 ---- 24 H -0.037 Total Mulliken Charge = 0.000 ! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 26.33 PRESS = 0.0 ! Etot = -1014.5269 EKtot = 50.2378 EPtot = -1064.7648 ! BOND = 17.2016 ANGLE = 70.1313 DIHED = 180.5507 ! 1-4 NB = 175.8059 1-4 EEL = 1427.2611 VDWAALS = -261.1028 ! EELEC = -2616.9366 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.6759 ------------------------------------------------------------------------------ ! Atomic Charges for Step 6 : Atom Element Mulliken Charge 1 N -0.528 2 H 0.253 *************** *** 412,426 **** 24 H -0.034 Total Mulliken Charge = 0.000 ! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 26.33 PRESS = 0.0 ! Etot = -1014.5269 EKtot = 50.2378 EPtot = -1064.7648 ! BOND = 17.2016 ANGLE = 70.1313 DIHED = 180.5507 ! 1-4 NB = 175.8059 1-4 EEL = 1427.2611 VDWAALS = -261.1028 ! EELEC = -2616.9366 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.6759 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.524 2 H 0.257 --- 449,463 ---- 24 H -0.034 Total Mulliken Charge = 0.000 ! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 31.97 PRESS = 0.0 ! Etot = -1020.4249 EKtot = 60.9969 EPtot = -1081.4219 ! BOND = 16.8927 ANGLE = 71.1040 DIHED = 180.2312 ! 1-4 NB = 174.9129 1-4 EEL = 1423.0567 VDWAALS = -265.6116 ! EELEC = -2623.6795 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -58.3282 ------------------------------------------------------------------------------ ! Atomic Charges for Step 7 : Atom Element Mulliken Charge 1 N -0.524 2 H 0.257 *************** *** 448,462 **** 24 H -0.032 Total Mulliken Charge = 0.000 ! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 31.97 PRESS = 0.0 ! Etot = -1020.4249 EKtot = 60.9969 EPtot = -1081.4219 ! BOND = 16.8927 ANGLE = 71.1040 DIHED = 180.2312 ! 1-4 NB = 174.9129 1-4 EEL = 1423.0567 VDWAALS = -265.6116 ! EELEC = -2623.6795 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -58.3282 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.521 2 H 0.261 --- 485,499 ---- 24 H -0.032 Total Mulliken Charge = 0.000 ! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 37.63 PRESS = 0.0 ! Etot = -1041.5279 EKtot = 71.7916 EPtot = -1113.3195 ! BOND = 14.5046 ANGLE = 73.5833 DIHED = 180.1474 ! 1-4 NB = 174.1622 1-4 EEL = 1418.7580 VDWAALS = -270.2601 ! EELEC = -2645.7019 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -58.5128 ------------------------------------------------------------------------------ ! Atomic Charges for Step 8 : Atom Element Mulliken Charge 1 N -0.521 2 H 0.261 *************** *** 484,498 **** 24 H -0.033 Total Mulliken Charge = 0.000 ! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 37.63 PRESS = 0.0 ! Etot = -1041.5279 EKtot = 71.7916 EPtot = -1113.3195 ! BOND = 14.5046 ANGLE = 73.5833 DIHED = 180.1474 ! 1-4 NB = 174.1622 1-4 EEL = 1418.7580 VDWAALS = -270.2601 ! EELEC = -2645.7019 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -58.5128 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.519 2 H 0.266 --- 521,535 ---- 24 H -0.033 Total Mulliken Charge = 0.000 ! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 41.77 PRESS = 0.0 ! Etot = -1022.1868 EKtot = 79.6871 EPtot = -1101.8739 ! BOND = 12.7201 ANGLE = 77.2762 DIHED = 180.3778 ! 1-4 NB = 173.5346 1-4 EEL = 1414.3930 VDWAALS = -274.8841 ! EELEC = -2627.4968 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.7946 ------------------------------------------------------------------------------ ! Atomic Charges for Step 9 : Atom Element Mulliken Charge 1 N -0.519 2 H 0.266 *************** *** 520,534 **** 24 H -0.034 Total Mulliken Charge = 0.000 ! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 41.77 PRESS = 0.0 ! Etot = -1022.1868 EKtot = 79.6871 EPtot = -1101.8739 ! BOND = 12.7201 ANGLE = 77.2762 DIHED = 180.3778 ! 1-4 NB = 173.5346 1-4 EEL = 1414.3930 VDWAALS = -274.8841 ! EELEC = -2627.4968 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.7946 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.516 2 H 0.269 --- 557,571 ---- 24 H -0.034 Total Mulliken Charge = 0.000 ! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 43.76 PRESS = 0.0 ! Etot = -1017.4109 EKtot = 83.4735 EPtot = -1100.8845 ! BOND = 13.6907 ANGLE = 81.5791 DIHED = 180.9821 ! 1-4 NB = 172.9561 1-4 EEL = 1409.9428 VDWAALS = -279.3377 ! EELEC = -2624.0617 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -56.6357 ------------------------------------------------------------------------------ ! Atomic Charges for Step 10 : Atom Element Mulliken Charge 1 N -0.516 2 H 0.269 *************** *** 556,570 **** 24 H -0.036 Total Mulliken Charge = 0.000 ! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 43.76 PRESS = 0.0 ! Etot = -1017.4109 EKtot = 83.4735 EPtot = -1100.8845 ! BOND = 13.6907 ANGLE = 81.5791 DIHED = 180.9821 ! 1-4 NB = 172.9561 1-4 EEL = 1409.9428 VDWAALS = -279.3377 ! EELEC = -2624.0617 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -56.6357 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.513 2 H 0.268 --- 593,607 ---- 24 H -0.036 Total Mulliken Charge = 0.000 ! NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 44.78 PRESS = 0.0 ! Etot = -1001.1499 EKtot = 85.4272 EPtot = -1086.5771 ! BOND = 16.7729 ANGLE = 85.7186 DIHED = 181.9992 ! 1-4 NB = 172.3199 1-4 EEL = 1405.3931 VDWAALS = -283.5021 ! EELEC = -2609.0724 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -56.2064 ------------------------------------------------------------------------------ ! Atomic Charges for Step 11 : Atom Element Mulliken Charge 1 N -0.513 2 H 0.268 *************** *** 592,606 **** 24 H -0.039 Total Mulliken Charge = 0.000 ! NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 44.78 PRESS = 0.0 ! Etot = -1001.1499 EKtot = 85.4272 EPtot = -1086.5771 ! BOND = 16.7729 ANGLE = 85.7186 DIHED = 181.9992 ! 1-4 NB = 172.3199 1-4 EEL = 1405.3931 VDWAALS = -283.5021 ! EELEC = -2609.0724 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -56.2064 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.511 2 H 0.265 --- 629,643 ---- 24 H -0.039 Total Mulliken Charge = 0.000 ! NSTEP = 12 TIME(PS) = 0.012 TEMP(K) = 46.75 PRESS = 0.0 ! Etot = -1017.7592 EKtot = 89.1936 EPtot = -1106.9529 ! BOND = 19.4980 ANGLE = 88.9461 DIHED = 183.4461 ! 1-4 NB = 171.5210 1-4 EEL = 1400.7889 VDWAALS = -287.2846 ! EELEC = -2626.6153 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.2531 ------------------------------------------------------------------------------ ! Atomic Charges for Step 12 : Atom Element Mulliken Charge 1 N -0.511 2 H 0.265 *************** *** 628,642 **** 24 H -0.042 Total Mulliken Charge = 0.000 ! NSTEP = 12 TIME(PS) = 0.012 TEMP(K) = 46.75 PRESS = 0.0 ! Etot = -1017.7592 EKtot = 89.1936 EPtot = -1106.9529 ! BOND = 19.4980 ANGLE = 88.9461 DIHED = 183.4461 ! 1-4 NB = 171.5210 1-4 EEL = 1400.7889 VDWAALS = -287.2846 ! EELEC = -2626.6153 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -57.2531 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.509 2 H 0.260 --- 665,679 ---- 24 H -0.042 Total Mulliken Charge = 0.000 ! NSTEP = 13 TIME(PS) = 0.013 TEMP(K) = 50.35 PRESS = 0.0 ! Etot = -1041.4284 EKtot = 96.0584 EPtot = -1137.4868 ! BOND = 20.4725 ANGLE = 90.7423 DIHED = 185.3170 ! 1-4 NB = 170.4931 1-4 EEL = 1396.2477 VDWAALS = -290.6140 ! EELEC = -2650.8145 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -59.3308 ------------------------------------------------------------------------------ ! Atomic Charges for Step 13 : Atom Element Mulliken Charge 1 N -0.509 2 H 0.260 *************** *** 664,678 **** 24 H -0.044 Total Mulliken Charge = 0.000 ! NSTEP = 13 TIME(PS) = 0.013 TEMP(K) = 50.35 PRESS = 0.0 ! Etot = -1041.4284 EKtot = 96.0584 EPtot = -1137.4868 ! BOND = 20.4725 ANGLE = 90.7423 DIHED = 185.3170 ! 1-4 NB = 170.4931 1-4 EEL = 1396.2477 VDWAALS = -290.6140 ! EELEC = -2650.8145 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -59.3308 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.511 2 H 0.256 --- 701,715 ---- 24 H -0.044 Total Mulliken Charge = 0.000 ! NSTEP = 14 TIME(PS) = 0.014 TEMP(K) = 54.49 PRESS = 0.0 ! Etot = -1026.4938 EKtot = 103.9417 EPtot = -1130.4355 ! BOND = 20.8637 ANGLE = 90.9542 DIHED = 187.5781 ! 1-4 NB = 169.2326 1-4 EEL = 1391.9394 VDWAALS = -293.4506 ! EELEC = -2636.3163 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -61.2365 ------------------------------------------------------------------------------ ! Atomic Charges for Step 14 : Atom Element Mulliken Charge 1 N -0.511 2 H 0.256 *************** *** 700,714 **** 24 H -0.046 Total Mulliken Charge = 0.000 ! NSTEP = 14 TIME(PS) = 0.014 TEMP(K) = 54.49 PRESS = 0.0 ! Etot = -1026.4938 EKtot = 103.9417 EPtot = -1130.4355 ! BOND = 20.8637 ANGLE = 90.9542 DIHED = 187.5781 ! 1-4 NB = 169.2326 1-4 EEL = 1391.9394 VDWAALS = -293.4506 ! EELEC = -2636.3163 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -61.2365 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.515 2 H 0.253 --- 737,751 ---- 24 H -0.046 Total Mulliken Charge = 0.000 ! NSTEP = 15 TIME(PS) = 0.015 TEMP(K) = 57.68 PRESS = 0.0 ! Etot = -1029.0856 EKtot = 110.0322 EPtot = -1139.1177 ! BOND = 22.8946 ANGLE = 89.8134 DIHED = 190.1632 ! 1-4 NB = 167.7979 1-4 EEL = 1388.0432 VDWAALS = -295.8018 ! EELEC = -2639.5471 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -62.4812 ------------------------------------------------------------------------------ ! Atomic Charges for Step 15 : Atom Element Mulliken Charge 1 N -0.515 2 H 0.253 *************** *** 736,750 **** 24 H -0.047 Total Mulliken Charge = 0.000 ! NSTEP = 15 TIME(PS) = 0.015 TEMP(K) = 57.68 PRESS = 0.0 ! Etot = -1029.0856 EKtot = 110.0322 EPtot = -1139.1177 ! BOND = 22.8946 ANGLE = 89.8134 DIHED = 190.1632 ! 1-4 NB = 167.7979 1-4 EEL = 1388.0432 VDWAALS = -295.8018 ! EELEC = -2639.5471 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -62.4812 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.522 2 H 0.254 --- 773,787 ---- 24 H -0.047 Total Mulliken Charge = 0.000 ! NSTEP = 16 TIME(PS) = 0.016 TEMP(K) = 59.53 PRESS = 0.0 ! Etot = -1044.5076 EKtot = 113.5716 EPtot = -1158.0792 ! BOND = 27.1392 ANGLE = 87.8359 DIHED = 192.9775 ! 1-4 NB = 166.2853 1-4 EEL = 1384.6904 VDWAALS = -297.7257 ! EELEC = -2655.9995 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -63.2822 ------------------------------------------------------------------------------ ! Atomic Charges for Step 16 : Atom Element Mulliken Charge 1 N -0.522 2 H 0.254 *************** *** 772,786 **** 24 H -0.048 Total Mulliken Charge = 0.000 ! NSTEP = 16 TIME(PS) = 0.016 TEMP(K) = 59.53 PRESS = 0.0 ! Etot = -1044.5076 EKtot = 113.5716 EPtot = -1158.0792 ! BOND = 27.1392 ANGLE = 87.8359 DIHED = 192.9775 ! 1-4 NB = 166.2853 1-4 EEL = 1384.6904 VDWAALS = -297.7257 ! EELEC = -2655.9995 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -63.2822 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.530 2 H 0.256 --- 809,823 ---- 24 H -0.048 Total Mulliken Charge = 0.000 ! NSTEP = 17 TIME(PS) = 0.017 TEMP(K) = 60.87 PRESS = 0.0 ! Etot = -1047.0289 EKtot = 116.1272 EPtot = -1163.1561 ! BOND = 31.6487 ANGLE = 85.6547 DIHED = 195.9111 ! 1-4 NB = 164.7943 1-4 EEL = 1381.9024 VDWAALS = -299.3090 ! EELEC = -2659.6349 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -64.1235 ------------------------------------------------------------------------------ ! Atomic Charges for Step 17 : Atom Element Mulliken Charge 1 N -0.530 2 H 0.256 *************** *** 808,822 **** 24 H -0.047 Total Mulliken Charge = 0.000 ! NSTEP = 17 TIME(PS) = 0.017 TEMP(K) = 60.87 PRESS = 0.0 ! Etot = -1047.0289 EKtot = 116.1272 EPtot = -1163.1561 ! BOND = 31.6487 ANGLE = 85.6547 DIHED = 195.9111 ! 1-4 NB = 164.7943 1-4 EEL = 1381.9024 VDWAALS = -299.3090 ! EELEC = -2659.6349 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -64.1235 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.538 2 H 0.259 --- 845,859 ---- 24 H -0.047 Total Mulliken Charge = 0.000 ! NSTEP = 18 TIME(PS) = 0.018 TEMP(K) = 62.74 PRESS = 0.0 ! Etot = -1069.0538 EKtot = 119.6954 EPtot = -1188.7492 ! BOND = 33.8303 ANGLE = 83.8451 DIHED = 198.8572 ! 1-4 NB = 163.3989 1-4 EEL = 1379.5950 VDWAALS = -300.6363 ! EELEC = -2682.7245 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -64.9149 ------------------------------------------------------------------------------ ! Atomic Charges for Step 18 : Atom Element Mulliken Charge 1 N -0.538 2 H 0.259 *************** *** 844,858 **** 24 H -0.044 Total Mulliken Charge = 0.000 ! NSTEP = 18 TIME(PS) = 0.018 TEMP(K) = 62.74 PRESS = 0.0 ! Etot = -1069.0538 EKtot = 119.6954 EPtot = -1188.7492 ! BOND = 33.8303 ANGLE = 83.8451 DIHED = 198.8572 ! 1-4 NB = 163.3989 1-4 EEL = 1379.5950 VDWAALS = -300.6363 ! EELEC = -2682.7245 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -64.9149 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.544 2 H 0.261 --- 881,895 ---- 24 H -0.044 Total Mulliken Charge = 0.000 ! NSTEP = 19 TIME(PS) = 0.019 TEMP(K) = 65.25 PRESS = 0.0 ! Etot = -1066.4117 EKtot = 124.4730 EPtot = -1190.8847 ! BOND = 33.0115 ANGLE = 82.8070 DIHED = 201.7218 ! 1-4 NB = 162.1305 1-4 EEL = 1377.5888 VDWAALS = -301.7698 ! EELEC = -2680.9436 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -65.4308 ------------------------------------------------------------------------------ ! Atomic Charges for Step 19 : Atom Element Mulliken Charge 1 N -0.544 2 H 0.261 *************** *** 880,894 **** 24 H -0.040 Total Mulliken Charge = 0.000 ! NSTEP = 19 TIME(PS) = 0.019 TEMP(K) = 65.25 PRESS = 0.0 ! Etot = -1066.4117 EKtot = 124.4730 EPtot = -1190.8847 ! BOND = 33.0115 ANGLE = 82.8070 DIHED = 201.7218 ! 1-4 NB = 162.1305 1-4 EEL = 1377.5888 VDWAALS = -301.7698 ! EELEC = -2680.9436 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -65.4308 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.547 2 H 0.261 --- 917,931 ---- 24 H -0.040 Total Mulliken Charge = 0.000 ! NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 67.34 PRESS = 0.0 ! Etot = -1056.9459 EKtot = 128.4633 EPtot = -1185.4092 ! BOND = 30.9914 ANGLE = 82.7138 DIHED = 204.4274 ! 1-4 NB = 160.9728 1-4 EEL = 1375.6649 VDWAALS = -302.7514 ! EELEC = -2672.0888 EHBOND = 0.0000 RESTRAINT = 0.0000 ! AM1ESCF= -65.3393 ------------------------------------------------------------------------------ ! Atomic Charges for Step 20 : Atom Element Mulliken Charge 1 N -0.547 2 H 0.261 *************** *** 916,930 **** 24 H -0.035 Total Mulliken Charge = 0.000 - NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 67.34 PRESS = 0.0 - Etot = -1056.9459 EKtot = 128.4633 EPtot = -1185.4092 - BOND = 30.9914 ANGLE = 82.7138 DIHED = 204.4274 - 1-4 NB = 160.9728 1-4 EEL = 1375.6649 VDWAALS = -302.7514 - EELEC = -2672.0888 EHBOND = 0.0000 RESTRAINT = 0.0000 - AM1ESCF= -65.3393 - ------------------------------------------------------------------------------ - - A V E R A G E S O V E R 20 S T E P S --- 953,958 ---- *************** *** 953,1008 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.33% of Total) ! | Build the list 0.02 (94.56% of List ) ! | Other 0.00 ( 5.44% of List ) ! | List time 0.02 ( 9.09% of Nonbo) ! | Short_ene time 0.19 (99.70% of Direc) ! | Other 0.00 ( 0.30% of Direc) ! | Direct Ewald time 0.19 (98.32% of Ewald) ! | Force Adjust 0.00 ( 1.55% of Ewald) ! | Virial junk 0.00 ( 0.03% of Ewald) ! | Start sycnronization 0.00 ( 0.02% of Ewald) ! | Other 0.00 ( 0.07% of Ewald) ! | Ewald time 0.19 (90.86% of Nonbo) ! | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Other 0.00 ( 0.03% of Nonbo) ! | Nonbond force 0.21 (23.20% of Force) ! | QMMM setup 0.00 ( 0.26% of QMMM ) ! | QMMM list build 0.00 ( 0.13% of QMMM ) ! | QMMM prep coords 0.00 ( 0.09% of QMMM ) ! | QMMM RIJ Eqns Calc 0.06 ( 8.74% of QMMM ) ! | QMMM hcore QM-QM 0.03 (48.39% of QMMM ) ! | QMMM hcore QM-MM 0.03 (51.53% of QMMM ) ! | Other 0.00 ( 0.08% of QMMM ) ! | QMMM hcore calc 0.07 (14.10% of QMMM ) ! | QMMM fock build 0.05 (13.38% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 0.51% of QMMM ) ! | QMMM full matrix dia 0.20 (50.40% of QMMM ) ! | QMMM pseudo matrix d 0.09 (21.57% of QMMM ) ! | QMMM density build 0.05 (13.78% of QMMM ) ! | Other 0.00 ( 0.35% of QMMM ) ! | QMMM scf 0.40 (85.78% of QMMM ) ! | Other 0.00 ( 0.12% of QMMM ) ! | QMMM energy 0.46 (67.22% of QMMM ) ! | QMMM QM-QM force 0.05 ( 7.74% of QMMM ) ! | QMMM QM-MM force 0.10 (14.74% of QMMM ) ! | QMMM Mulliken Chgs 0.01 ( 0.99% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.05% of QMMM ) ! | Other 0.00 ( 0.04% of QMMM ) ! | QMMM 0.69 (74.69% of Force) ! | Bond/Angle/Dihedral 0.02 ( 2.08% of Force) ! | Other 0.00 ( 0.03% of Force) ! | Force time 0.92 (93.16% of Runmd) ! | Verlet update time 0.06 ( 6.42% of Runmd) ! | Other 0.00 ( 0.42% of Runmd) ! | Runmd Time 0.99 (93.72% of Total) ! | Other 0.06 ( 5.95% of Total) ! | Total time 1.06 (100.0% of ALL ) | Highest rstack allocated: 2400 | Highest istack allocated: 480 ! | Job began at 14:08:48.198 on 03/09/2006 ! | Setup done at 14:08:48.265 on 03/09/2006 ! | Run done at 14:08:49.257 on 03/09/2006 ! | wallclock() was called 5036 times --- 981,1034 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.16% of Total) ! | Build the list 0.01 (95.70% of List ) ! | Other 0.00 ( 4.30% of List ) ! | List time 0.01 ( 3.75% of Nonbo) ! | Short_ene time 0.21 (99.84% of Direc) ! | Other 0.00 ( 0.16% of Direc) ! | Direct Ewald time 0.21 (98.44% of Ewald) ! | Force Adjust 0.00 ( 1.50% of Ewald) ! | Virial junk 0.00 ( 0.01% of Ewald) ! | Start sycnronization 0.00 ( 0.01% of Ewald) ! | Other 0.00 ( 0.03% of Ewald) ! | Ewald time 0.21 (96.23% of Nonbo) ! | Other 0.00 ( 0.02% of Nonbo) ! | Nonbond force 0.22 (26.27% of Force) ! | QMMM setup 0.00 ( 0.17% of QMMM ) ! | QMMM list build 0.00 ( 0.12% of QMMM ) ! | QMMM prep coords 0.00 ( 0.04% of QMMM ) ! | QMMM RIJ Eqns Calc 0.06 ( 9.34% of QMMM ) ! | QMMM hcore QM-QM 0.03 (58.16% of QMMM ) ! | QMMM hcore QM-MM 0.02 (41.80% of QMMM ) ! | Other 0.00 ( 0.04% of QMMM ) ! | QMMM hcore calc 0.05 (12.39% of QMMM ) ! | QMMM fock build 0.03 ( 9.66% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 0.53% of QMMM ) ! | QMMM full matrix dia 0.20 (54.92% of QMMM ) ! | QMMM pseudo matrix d 0.08 (22.24% of QMMM ) ! | QMMM density build 0.04 (12.38% of QMMM ) ! | Other 0.00 ( 0.27% of QMMM ) ! | QMMM scf 0.36 (87.57% of QMMM ) ! | Other 0.00 ( 0.04% of QMMM ) ! | QMMM energy 0.41 (67.48% of QMMM ) ! | QMMM QM-QM force 0.05 ( 8.44% of QMMM ) ! | QMMM QM-MM force 0.09 (14.35% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM 0.60 (71.47% of Force) ! | Bond/Angle/Dihedral 0.02 ( 2.25% of Force) ! | Other 0.00 ( 0.02% of Force) ! | Force time 0.84 (98.55% of Runmd) ! | Verlet update time 0.01 ( 1.39% of Runmd) ! | Other 0.00 ( 0.06% of Runmd) ! | Runmd Time 0.86 (98.01% of Total) ! | Other 0.02 ( 1.83% of Total) ! | Total time 0.87 (100.0% of ALL ) | Highest rstack allocated: 2400 | Highest istack allocated: 480 ! | Job began at 13:17:45.529 on 04/17/2007 ! | Setup done at 13:17:45.547 on 04/17/2007 ! | Run done at 13:17:46.403 on 04/17/2007 ! | wallclock() was called 5038 times *** test/qmmm2/lysine_PM3_calc_mulliken/lysine_md.out.save 2006-04-03 18:14:18.000000000 -0700 --- test/qmmm2/lysine_PM3_calc_mulliken/lysine_md.out.save 2007-04-17 13:22:44.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/09/2006 at 14:08:44 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 13:17:43 [-O]verwriting output File Assignments: *************** *** 154,159 **** --- 154,160 ---- | QMMM: QM Atom Mask : 44 bytes | QMMM: QM Coordinate Arrays : 824 bytes | QMMM: Scaled MM Charge Array : 176 bytes + | QMMM: SCF Mulliken Charge Storage : 40 bytes | QMMM: QM Force Arrays : 648 bytes | QMMM: Density Matrix : 288 bytes | QMMM: Density Matrix Copies : 576 bytes *************** *** 193,205 **** PM3ESCF= -10.9711 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.116 ! 2 H 0.041 ! 3 H 0.049 ! 4 H 0.067 ! 5 H -0.042 Total Mulliken Charge = 0.000 NSTEP = 2 TIME(PS) = 0.402 TEMP(K) = 361.03 PRESS = 0.0 --- 194,206 ---- PM3ESCF= -10.9711 ------------------------------------------------------------------------------ ! Atomic Charges for Step 1 : Atom Element Mulliken Charge ! 1 C -0.108 ! 2 H 0.038 ! 3 H 0.046 ! 4 H 0.070 ! 5 H -0.046 Total Mulliken Charge = 0.000 NSTEP = 2 TIME(PS) = 0.402 TEMP(K) = 361.03 PRESS = 0.0 *************** *** 210,222 **** PM3ESCF= -12.0125 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.124 ! 2 H 0.045 ! 3 H 0.052 ! 4 H 0.065 ! 5 H -0.037 Total Mulliken Charge = 0.000 NSTEP = 3 TIME(PS) = 0.403 TEMP(K) = 342.94 PRESS = 0.0 --- 211,223 ---- PM3ESCF= -12.0125 ------------------------------------------------------------------------------ ! Atomic Charges for Step 2 : Atom Element Mulliken Charge ! 1 C -0.116 ! 2 H 0.041 ! 3 H 0.049 ! 4 H 0.067 ! 5 H -0.042 Total Mulliken Charge = 0.000 NSTEP = 3 TIME(PS) = 0.403 TEMP(K) = 342.94 PRESS = 0.0 *************** *** 227,239 **** PM3ESCF= -11.8264 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.130 ! 2 H 0.046 ! 3 H 0.054 ! 4 H 0.063 ! 5 H -0.033 Total Mulliken Charge = 0.000 NSTEP = 4 TIME(PS) = 0.404 TEMP(K) = 307.22 PRESS = 0.0 --- 228,240 ---- PM3ESCF= -11.8264 ------------------------------------------------------------------------------ ! Atomic Charges for Step 3 : Atom Element Mulliken Charge ! 1 C -0.124 ! 2 H 0.045 ! 3 H 0.052 ! 4 H 0.065 ! 5 H -0.037 Total Mulliken Charge = 0.000 NSTEP = 4 TIME(PS) = 0.404 TEMP(K) = 307.22 PRESS = 0.0 *************** *** 244,256 **** PM3ESCF= -10.6843 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.133 2 H 0.046 3 H 0.054 ! 4 H 0.061 ! 5 H -0.029 Total Mulliken Charge = 0.000 NSTEP = 5 TIME(PS) = 0.405 TEMP(K) = 298.20 PRESS = 0.0 --- 245,257 ---- PM3ESCF= -10.6843 ------------------------------------------------------------------------------ ! Atomic Charges for Step 4 : Atom Element Mulliken Charge ! 1 C -0.130 2 H 0.046 3 H 0.054 ! 4 H 0.063 ! 5 H -0.033 Total Mulliken Charge = 0.000 NSTEP = 5 TIME(PS) = 0.405 TEMP(K) = 298.20 PRESS = 0.0 *************** *** 261,266 **** --- 262,275 ---- PM3ESCF= -9.9213 ------------------------------------------------------------------------------ + Atomic Charges for Step 5 : + Atom Element Mulliken Charge + 1 C -0.133 + 2 H 0.046 + 3 H 0.054 + 4 H 0.061 + 5 H -0.029 + Total Mulliken Charge = 0.000 A V E R A G E S O V E R 5 S T E P S *************** *** 291,339 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.18% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) | Calc gb off-diag 0.00 (70.69% of Gen B) | Other 0.00 (29.31% of Gen B) ! | Gen Born time 0.00 (97.29% of Nonbo) ! | IPS excludes 0.00 ( 2.71% of Nonbo) ! | Nonbond force 0.00 ( 5.45% of Force) ! | QMMM setup 0.00 (30.29% of QMMM ) ! | QMMM list build 0.00 ( 0.64% of QMMM ) ! | QMMM prep coords 0.00 ( 4.64% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 3.34% of QMMM ) ! | QMMM hcore QM-QM 0.00 (83.30% of QMMM ) ! | QMMM hcore QM-MM 0.00 (14.03% of QMMM ) ! | Other 0.00 ( 2.67% of QMMM ) ! | QMMM hcore calc 0.00 (24.61% of QMMM ) ! | QMMM fock build 0.00 (17.83% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 5.56% of QMMM ) ! | QMMM full matrix dia 0.00 (29.54% of QMMM ) ! | QMMM pseudo matrix d 0.00 (14.09% of QMMM ) ! | QMMM density build 0.00 (11.12% of QMMM ) ! | Other 0.00 (21.85% of QMMM ) ! | QMMM scf 0.00 (72.43% of QMMM ) ! | QMMM GB energy 0.00 ( 1.40% of QMMM ) ! | Other 0.00 ( 1.56% of QMMM ) ! | QMMM energy 0.00 (35.25% of QMMM ) ! | QMMM QM-QM force 0.00 ( 7.31% of QMMM ) ! | QMMM QM-MM force 0.00 ( 3.48% of QMMM ) ! | QMMM Mulliken Chgs 0.00 (12.74% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.70% of QMMM ) ! | Other 0.00 ( 1.62% of QMMM ) ! | QMMM 0.00 (84.94% of Force) ! | Bond/Angle/Dihedral 0.00 ( 9.32% of Force) ! | Other 0.00 ( 0.29% of Force) ! | Force time 0.00 ( 1.09% of Runmd) ! | Verlet update time 0.03 ( 8.23% of Runmd) ! | Other 0.34 (90.68% of Runmd) ! | Runmd Time 0.37 (96.73% of Total) ! | Other 0.01 ( 3.08% of Total) ! | Total time 0.38 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:08:44.521 on 03/09/2006 ! | Setup done at 14:08:44.533 on 03/09/2006 ! | Run done at 14:08:44.906 on 03/09/2006 ! | wallclock() was called 778 times --- 300,347 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 3.82% of Total) ! | Fast Water setup 0.00 ( 0.12% of Total) | Calc gb off-diag 0.00 (70.69% of Gen B) | Other 0.00 (29.31% of Gen B) ! | Gen Born time 0.00 (99.28% of Nonbo) ! | IPS excludes 0.00 ( 0.72% of Nonbo) ! | Nonbond force 0.00 ( 5.80% of Force) ! | QMMM setup 0.00 (31.26% of QMMM ) ! | QMMM list build 0.00 ( 0.73% of QMMM ) ! | QMMM prep coords 0.00 ( 3.13% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 4.05% of QMMM ) ! | QMMM hcore QM-QM 0.00 (88.60% of QMMM ) ! | QMMM hcore QM-MM 0.00 (10.97% of QMMM ) ! | Other 0.00 ( 0.43% of QMMM ) ! | QMMM hcore calc 0.00 (24.22% of QMMM ) ! | QMMM fock build 0.00 (13.73% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 4.07% of QMMM ) ! | QMMM full matrix dia 0.00 (37.64% of QMMM ) ! | QMMM pseudo matrix d 0.00 (15.34% of QMMM ) ! | QMMM density build 0.00 (10.13% of QMMM ) ! | Other 0.00 (19.09% of QMMM ) ! | QMMM scf 0.00 (73.43% of QMMM ) ! | QMMM GB energy 0.00 ( 1.17% of QMMM ) ! | Other 0.00 ( 1.17% of QMMM ) ! | QMMM energy 0.00 (45.97% of QMMM ) ! | QMMM QM-QM force 0.00 ( 9.04% of QMMM ) ! | QMMM QM-MM force 0.00 ( 3.96% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.59% of QMMM ) ! | Other 0.00 ( 1.27% of QMMM ) ! | QMMM 0.00 (84.14% of Force) ! | Bond/Angle/Dihedral 0.00 ( 9.90% of Force) ! | Other 0.00 ( 0.16% of Force) ! | Force time 0.00 (59.75% of Runmd) ! | Verlet update time 0.00 (35.04% of Runmd) ! | Other 0.00 ( 5.21% of Runmd) ! | Runmd Time 0.00 (59.08% of Total) ! | Other 0.00 (36.99% of Total) ! | Total time 0.01 (98.87% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 13:17:43.097 on 04/17/2007 ! | Setup done at 13:17:43.100 on 04/17/2007 ! | Run done at 13:17:43.105 on 04/17/2007 ! | wallclock() was called 780 times *** test/qmmm2/lysine_PM3_calc_mulliken/lysine.out.save 2006-04-03 18:14:18.000000000 -0700 --- test/qmmm2/lysine_PM3_calc_mulliken/lysine.out.save 2007-04-17 13:22:49.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/09/2006 at 14:08:44 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 13:17:42 [-O]verwriting output File Assignments: *************** *** 152,157 **** --- 152,158 ---- | QMMM: QM Atom Mask : 44 bytes | QMMM: QM Coordinate Arrays : 824 bytes | QMMM: Scaled MM Charge Array : 176 bytes + | QMMM: SCF Mulliken Charge Storage : 40 bytes | QMMM: QM Force Arrays : 648 bytes | QMMM: Density Matrix : 288 bytes | QMMM: Density Matrix Copies : 576 bytes *************** *** 182,195 **** 4. RESULTS -------------------------------------------------------------------------------- - Atomic Charges: - Atom Element Mulliken Charge - 1 C -0.113 - 2 H 0.027 - 3 H 0.049 - 4 H 0.074 - 5 H -0.036 - Total Mulliken Charge = 0.000 NSTEP ENERGY RMS GMAX NAME NUMBER --- 183,188 ---- *************** *** 199,205 **** VDWAALS = 0.1908 EEL = -4.1241 EGB = 0.0000 1-4 VDW = 3.7051 1-4 EEL = 65.9137 RESTRAINT = 0.0000 PM3ESCF = -12.5570 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 --- 192,198 ---- VDWAALS = 0.1908 EEL = -4.1241 EGB = 0.0000 1-4 VDW = 3.7051 1-4 EEL = 65.9137 RESTRAINT = 0.0000 PM3ESCF = -12.5570 ! Atomic Charges for Step 1 : Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 *************** *** 216,222 **** VDWAALS = 0.1641 EEL = -4.1515 EGB = 0.0000 1-4 VDW = 3.6656 1-4 EEL = 65.8795 RESTRAINT = 0.0000 PM3ESCF = -12.5644 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 --- 209,215 ---- VDWAALS = 0.1641 EEL = -4.1515 EGB = 0.0000 1-4 VDW = 3.6656 1-4 EEL = 65.8795 RESTRAINT = 0.0000 PM3ESCF = -12.5644 ! Atomic Charges for Step 2 : Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 *************** *** 233,239 **** VDWAALS = 0.1323 EEL = -4.1810 EGB = 0.0000 1-4 VDW = 3.6173 1-4 EEL = 65.8357 RESTRAINT = 0.0000 PM3ESCF = -12.5722 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 --- 226,232 ---- VDWAALS = 0.1323 EEL = -4.1810 EGB = 0.0000 1-4 VDW = 3.6173 1-4 EEL = 65.8357 RESTRAINT = 0.0000 PM3ESCF = -12.5722 ! Atomic Charges for Step 3 : Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 *************** *** 250,262 **** VDWAALS = 0.0952 EEL = -4.2103 EGB = 0.0000 1-4 VDW = 3.5597 1-4 EEL = 65.7813 RESTRAINT = 0.0000 PM3ESCF = -12.5801 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 3 H 0.049 4 H 0.074 ! 5 H -0.037 Total Mulliken Charge = 0.000 --- 243,255 ---- VDWAALS = 0.0952 EEL = -4.2103 EGB = 0.0000 1-4 VDW = 3.5597 1-4 EEL = 65.7813 RESTRAINT = 0.0000 PM3ESCF = -12.5801 ! Atomic Charges for Step 4 : Atom Element Mulliken Charge 1 C -0.113 2 H 0.027 3 H 0.049 4 H 0.074 ! 5 H -0.036 Total Mulliken Charge = 0.000 *************** *** 267,272 **** --- 260,273 ---- VDWAALS = 0.0531 EEL = -4.2368 EGB = 0.0000 1-4 VDW = 3.4941 1-4 EEL = 65.7184 RESTRAINT = 0.0000 PM3ESCF = -12.5877 + Atomic Charges for Step 5 : + Atom Element Mulliken Charge + 1 C -0.113 + 2 H 0.027 + 3 H 0.049 + 4 H 0.074 + 5 H -0.037 + Total Mulliken Charge = 0.000 Maximum number of minimization cycles reached. *************** *** 288,334 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 1.95% of Total) ! | Fast Water setup 0.00 ( 0.07% of Total) | Calc gb off-diag 0.00 (71.93% of Gen B) | Other 0.00 (28.07% of Gen B) ! | Gen Born time 0.00 (98.76% of Nonbo) ! | IPS excludes 0.00 ( 1.24% of Nonbo) ! | Nonbond force 0.00 ( 5.96% of Force) ! | QMMM setup 0.00 (29.41% of QMMM ) ! | QMMM list build 0.00 ( 0.55% of QMMM ) ! | QMMM prep coords 0.00 ( 4.25% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 2.98% of QMMM ) ! | QMMM hcore QM-QM 0.00 (83.10% of QMMM ) ! | QMMM hcore QM-MM 0.00 (14.92% of QMMM ) ! | Other 0.00 ( 1.99% of QMMM ) ! | QMMM hcore calc 0.00 (26.27% of QMMM ) ! | QMMM fock build 0.00 (16.87% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 4.26% of QMMM ) ! | QMMM full matrix dia 0.00 (35.19% of QMMM ) ! | QMMM pseudo matrix d 0.00 (10.81% of QMMM ) ! | QMMM density build 0.00 (11.64% of QMMM ) ! | Other 0.00 (21.22% of QMMM ) ! | QMMM scf 0.00 (70.20% of QMMM ) | QMMM GB energy 0.00 ( 1.24% of QMMM ) ! | Other 0.00 ( 2.29% of QMMM ) ! | QMMM energy 0.00 (33.53% of QMMM ) ! | QMMM QM-QM force 0.00 ( 7.74% of QMMM ) ! | QMMM QM-MM force 0.00 ( 3.86% of QMMM ) ! | QMMM Mulliken Chgs 0.00 (15.19% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.74% of QMMM ) ! | Other 0.00 ( 1.76% of QMMM ) ! | QMMM 0.00 (84.69% of Force) ! | Bond/Angle/Dihedral 0.00 ( 8.96% of Force) ! | Other 0.00 ( 0.39% of Force) ! | Force time 0.01 (100.0% of Runmd) ! | Runmd Time 0.01 (12.98% of Total) ! | Other 0.04 (84.99% of Total) ! | Total time 0.04 (99.61% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:08:44.298 on 03/09/2006 ! | Setup done at 14:08:44.322 on 03/09/2006 ! | Run done at 14:08:44.340 on 03/09/2006 ! | wallclock() was called 658 times --- 289,334 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 4.20% of Total) ! | Fast Water setup 0.00 ( 0.11% of Total) | Calc gb off-diag 0.00 (71.93% of Gen B) | Other 0.00 (28.07% of Gen B) ! | Gen Born time 0.00 (98.60% of Nonbo) ! | IPS excludes 0.00 ( 1.40% of Nonbo) ! | Nonbond force 0.00 ( 6.27% of Force) ! | QMMM setup 0.00 (31.82% of QMMM ) ! | QMMM list build 0.00 ( 0.75% of QMMM ) ! | QMMM prep coords 0.00 ( 3.52% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 4.59% of QMMM ) ! | QMMM hcore QM-QM 0.00 (86.13% of QMMM ) ! | QMMM hcore QM-MM 0.00 (12.38% of QMMM ) ! | Other 0.00 ( 1.49% of QMMM ) ! | QMMM hcore calc 0.00 (25.06% of QMMM ) ! | QMMM fock build 0.00 (13.04% of QMMM ) ! | QMMM elec-energy cal 0.00 ( 3.61% of QMMM ) ! | QMMM full matrix dia 0.00 (43.47% of QMMM ) ! | QMMM pseudo matrix d 0.00 (12.72% of QMMM ) ! | QMMM density build 0.00 ( 8.59% of QMMM ) ! | Other 0.00 (18.57% of QMMM ) ! | QMMM scf 0.00 (72.20% of QMMM ) | QMMM GB energy 0.00 ( 1.24% of QMMM ) ! | Other 0.00 ( 1.49% of QMMM ) ! | QMMM energy 0.00 (43.03% of QMMM ) ! | QMMM QM-QM force 0.00 ( 9.99% of QMMM ) ! | QMMM QM-MM force 0.00 ( 4.21% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.70% of QMMM ) ! | Other 0.00 ( 1.39% of QMMM ) ! | QMMM 0.00 (83.36% of Force) ! | Bond/Angle/Dihedral 0.00 (10.23% of Force) ! | Other 0.00 ( 0.13% of Force) ! | Force time 0.00 (100.0% of Runmd) ! | Runmd Time 0.00 (34.46% of Total) ! | Other 0.00 (61.23% of Total) ! | Total time 0.01 (98.95% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 13:17:42.981 on 04/17/2007 ! | Setup done at 13:17:42.984 on 04/17/2007 ! | Run done at 13:17:42.987 on 04/17/2007 ! | wallclock() was called 628 times *** test/qmmm_DFTB/crambin_2_DFTB/crambin_md_calc_mulliken.out.save 2006-04-03 18:15:16.000000000 -0700 --- test/qmmm_DFTB/crambin_2_DFTB/crambin_md_calc_mulliken.out.save 2007-04-17 14:12:25.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:20:54 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:33 [-O]verwriting output File Assignments: *************** *** 167,197 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (n ) 1 (n ) /usr/local/amber9/serial/dat/slko/nn.spl ! | 2 1 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 3 1 (n ) 3 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 4 1 (n ) 4 (s ) /usr/local/amber9/serial/dat/slko/ns.spl ! | 5 1 (n ) 5 (o ) /usr/local/amber9/serial/dat/slko/no.spl ! | 6 2 (h ) 1 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 8 2 (h ) 3 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 9 2 (h ) 4 (s ) /usr/local/amber9/serial/dat/slko/hs.spl ! | 10 2 (h ) 5 (o ) /usr/local/amber9/serial/dat/slko/ho.spl ! | 11 3 (c ) 1 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 12 3 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 13 3 (c ) 3 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 14 3 (c ) 4 (s ) /usr/local/amber9/serial/dat/slko/cs.spl ! | 15 3 (c ) 5 (o ) /usr/local/amber9/serial/dat/slko/co.spl ! | 16 4 (s ) 1 (n ) /usr/local/amber9/serial/dat/slko/sn.spl ! | 17 4 (s ) 2 (h ) /usr/local/amber9/serial/dat/slko/sh.spl ! | 18 4 (s ) 3 (c ) /usr/local/amber9/serial/dat/slko/sc.spl ! | 19 4 (s ) 4 (s ) /usr/local/amber9/serial/dat/slko/ss.spl ! | 20 4 (s ) 5 (o ) /usr/local/amber9/serial/dat/slko/so.spl ! | 21 5 (o ) 1 (n ) /usr/local/amber9/serial/dat/slko/on.spl ! | 22 5 (o ) 2 (h ) /usr/local/amber9/serial/dat/slko/oh.spl ! | 23 5 (o ) 3 (c ) /usr/local/amber9/serial/dat/slko/oc.spl ! | 24 5 (o ) 4 (s ) /usr/local/amber9/serial/dat/slko/os.spl ! | 25 5 (o ) 5 (o ) /usr/local/amber9/serial/dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 167,197 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (n ) 1 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl ! | 2 1 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 3 1 (n ) 3 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 4 1 (n ) 4 (s ) /usr/local/amber9_release/amber9_new//dat/slko/ns.spl ! | 5 1 (n ) 5 (o ) /usr/local/amber9_release/amber9_new//dat/slko/no.spl ! | 6 2 (h ) 1 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 8 2 (h ) 3 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 9 2 (h ) 4 (s ) /usr/local/amber9_release/amber9_new//dat/slko/hs.spl ! | 10 2 (h ) 5 (o ) /usr/local/amber9_release/amber9_new//dat/slko/ho.spl ! | 11 3 (c ) 1 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 12 3 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 13 3 (c ) 3 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 14 3 (c ) 4 (s ) /usr/local/amber9_release/amber9_new//dat/slko/cs.spl ! | 15 3 (c ) 5 (o ) /usr/local/amber9_release/amber9_new//dat/slko/co.spl ! | 16 4 (s ) 1 (n ) /usr/local/amber9_release/amber9_new//dat/slko/sn.spl ! | 17 4 (s ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/sh.spl ! | 18 4 (s ) 3 (c ) /usr/local/amber9_release/amber9_new//dat/slko/sc.spl ! | 19 4 (s ) 4 (s ) /usr/local/amber9_release/amber9_new//dat/slko/ss.spl ! | 20 4 (s ) 5 (o ) /usr/local/amber9_release/amber9_new//dat/slko/so.spl ! | 21 5 (o ) 1 (n ) /usr/local/amber9_release/amber9_new//dat/slko/on.spl ! | 22 5 (o ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/oh.spl ! | 23 5 (o ) 3 (c ) /usr/local/amber9_release/amber9_new//dat/slko/oc.spl ! | 24 5 (o ) 4 (s ) /usr/local/amber9_release/amber9_new//dat/slko/os.spl ! | 25 5 (o ) 5 (o ) /usr/local/amber9_release/amber9_new//dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 272,278 **** DFTBESCF= -2473.3214 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.497 2 H 0.238 --- 272,314 ---- DFTBESCF= -2473.3214 ------------------------------------------------------------------------------ ! Atomic Charges for Step 1 : ! Atom Element Mulliken Charge ! 1 N -0.497 ! 2 H 0.237 ! 3 C 0.084 ! 4 H 0.061 ! 5 C -0.058 ! 6 H 0.111 ! 7 H 0.034 ! 8 S -0.154 ! 9 C 0.320 ! 10 O -0.365 ! 11 N -0.481 ! 12 H 0.197 ! 13 C 0.085 ! 14 H 0.074 ! 15 C -0.064 ! 16 H 0.040 ! 17 H 0.062 ! 18 S -0.148 ! 19 C 0.339 ! 20 O -0.342 ! 21 H 0.268 ! 22 H -0.019 ! 23 H 0.308 ! 24 H -0.089 ! Total Mulliken Charge = 0.000 ! ! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 2.51 PRESS = 0.0 ! Etot = -3449.6831 EKtot = 4.7918 EPtot = -3454.4749 ! BOND = 17.0254 ANGLE = 75.4498 DIHED = 182.2630 ! 1-4 NB = 179.2821 1-4 EEL = 1439.3924 VDWAALS = -248.2132 ! EELEC = -2625.7841 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2473.8905 ! ------------------------------------------------------------------------------ ! ! Atomic Charges for Step 2 : Atom Element Mulliken Charge 1 N -0.497 2 H 0.238 *************** *** 300,314 **** 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 2.51 PRESS = 0.0 ! Etot = -3449.6831 EKtot = 4.7918 EPtot = -3454.4749 ! BOND = 17.0254 ANGLE = 75.4498 DIHED = 182.2630 ! 1-4 NB = 179.2821 1-4 EEL = 1439.3924 VDWAALS = -248.2132 ! EELEC = -2625.7841 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2473.8905 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.496 2 H 0.238 --- 336,350 ---- 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 7.86 PRESS = 0.0 ! Etot = -3447.6900 EKtot = 14.9974 EPtot = -3462.6873 ! BOND = 14.2893 ANGLE = 73.9451 DIHED = 181.9528 ! 1-4 NB = 178.7115 1-4 EEL = 1437.5225 VDWAALS = -250.3533 ! EELEC = -2623.6464 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2475.1090 ------------------------------------------------------------------------------ ! Atomic Charges for Step 3 : Atom Element Mulliken Charge 1 N -0.496 2 H 0.238 *************** *** 336,350 **** 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 7.86 PRESS = 0.0 ! Etot = -3447.6900 EKtot = 14.9974 EPtot = -3462.6873 ! BOND = 14.2893 ANGLE = 73.9451 DIHED = 181.9528 ! 1-4 NB = 178.7115 1-4 EEL = 1437.5225 VDWAALS = -250.3533 ! EELEC = -2623.6464 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2475.1090 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.495 2 H 0.239 --- 372,386 ---- 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 13.67 PRESS = 0.0 ! Etot = -3456.2592 EKtot = 26.0780 EPtot = -3482.3372 ! BOND = 13.3932 ANGLE = 72.0977 DIHED = 181.5037 ! 1-4 NB = 177.8948 1-4 EEL = 1434.6795 VDWAALS = -253.5142 ! EELEC = -2632.4018 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2475.9901 ------------------------------------------------------------------------------ ! Atomic Charges for Step 4 : Atom Element Mulliken Charge 1 N -0.495 2 H 0.239 *************** *** 372,386 **** 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 13.67 PRESS = 0.0 ! Etot = -3456.2592 EKtot = 26.0780 EPtot = -3482.3372 ! BOND = 13.3932 ANGLE = 72.0977 DIHED = 181.5037 ! 1-4 NB = 177.8948 1-4 EEL = 1434.6795 VDWAALS = -253.5142 ! EELEC = -2632.4018 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2475.9901 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.493 2 H 0.239 --- 408,422 ---- 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 18.86 PRESS = 0.0 ! Etot = -3451.7421 EKtot = 35.9847 EPtot = -3487.7268 ! BOND = 15.0446 ANGLE = 70.5877 DIHED = 180.9883 ! 1-4 NB = 176.9616 1-4 EEL = 1431.1168 VDWAALS = -257.3902 ! EELEC = -2628.4563 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2476.5792 ------------------------------------------------------------------------------ ! Atomic Charges for Step 5 : Atom Element Mulliken Charge 1 N -0.493 2 H 0.239 *************** *** 408,422 **** 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 18.86 PRESS = 0.0 ! Etot = -3451.7421 EKtot = 35.9847 EPtot = -3487.7268 ! BOND = 15.0446 ANGLE = 70.5877 DIHED = 180.9883 ! 1-4 NB = 176.9616 1-4 EEL = 1431.1168 VDWAALS = -257.3902 ! EELEC = -2628.4563 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2476.5792 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.489 2 H 0.239 --- 444,458 ---- 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 24.03 PRESS = 0.0 ! Etot = -3445.9008 EKtot = 45.8498 EPtot = -3491.7507 ! BOND = 16.9832 ANGLE = 70.0582 DIHED = 180.4948 ! 1-4 NB = 176.0352 1-4 EEL = 1427.0932 VDWAALS = -261.7277 ! EELEC = -2623.3498 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.3377 ------------------------------------------------------------------------------ ! Atomic Charges for Step 6 : Atom Element Mulliken Charge 1 N -0.489 2 H 0.239 *************** *** 444,458 **** 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 24.03 PRESS = 0.0 ! Etot = -3445.9008 EKtot = 45.8498 EPtot = -3491.7507 ! BOND = 16.9832 ANGLE = 70.0582 DIHED = 180.4948 ! 1-4 NB = 176.0352 1-4 EEL = 1427.0932 VDWAALS = -261.7277 ! EELEC = -2623.3498 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.3377 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.484 2 H 0.238 --- 480,494 ---- 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 29.87 PRESS = 0.0 ! Etot = -3463.3265 EKtot = 56.9884 EPtot = -3520.3150 ! BOND = 16.7160 ANGLE = 70.9422 DIHED = 180.1177 ! 1-4 NB = 175.2038 1-4 EEL = 1422.8237 VDWAALS = -266.3218 ! EELEC = -2641.5800 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.2166 ------------------------------------------------------------------------------ ! Atomic Charges for Step 7 : Atom Element Mulliken Charge 1 N -0.484 2 H 0.238 *************** *** 480,494 **** 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 29.87 PRESS = 0.0 ! Etot = -3463.3265 EKtot = 56.9884 EPtot = -3520.3150 ! BOND = 16.7160 ANGLE = 70.9422 DIHED = 180.1177 ! 1-4 NB = 175.2038 1-4 EEL = 1422.8237 VDWAALS = -266.3218 ! EELEC = -2641.5800 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.2166 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.479 2 H 0.238 --- 516,530 ---- 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 35.69 PRESS = 0.0 ! Etot = -3465.0175 EKtot = 68.0774 EPtot = -3533.0949 ! BOND = 14.4670 ANGLE = 73.3507 DIHED = 179.9486 ! 1-4 NB = 174.5023 1-4 EEL = 1418.4337 VDWAALS = -271.0009 ! EELEC = -2644.1677 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.6285 ------------------------------------------------------------------------------ ! Atomic Charges for Step 8 : Atom Element Mulliken Charge 1 N -0.479 2 H 0.238 *************** *** 516,530 **** 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 35.69 PRESS = 0.0 ! Etot = -3465.0175 EKtot = 68.0774 EPtot = -3533.0949 ! BOND = 14.4670 ANGLE = 73.3507 DIHED = 179.9486 ! 1-4 NB = 174.5023 1-4 EEL = 1418.4337 VDWAALS = -271.0009 ! EELEC = -2644.1677 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.6285 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.474 2 H 0.237 --- 552,566 ---- 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 39.97 PRESS = 0.0 ! Etot = -3455.4531 EKtot = 76.2541 EPtot = -3531.7071 ! BOND = 12.9023 ANGLE = 77.0212 DIHED = 180.0691 ! 1-4 NB = 173.9076 1-4 EEL = 1413.9688 VDWAALS = -275.6199 ! EELEC = -2635.7247 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.2316 ------------------------------------------------------------------------------ ! Atomic Charges for Step 9 : Atom Element Mulliken Charge 1 N -0.474 2 H 0.237 *************** *** 552,566 **** 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 39.97 PRESS = 0.0 ! Etot = -3455.4531 EKtot = 76.2541 EPtot = -3531.7071 ! BOND = 12.9023 ANGLE = 77.0212 DIHED = 180.0691 ! 1-4 NB = 173.9076 1-4 EEL = 1413.9688 VDWAALS = -275.6199 ! EELEC = -2635.7247 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.2316 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.470 2 H 0.237 --- 588,602 ---- 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 42.18 PRESS = 0.0 ! Etot = -3445.5332 EKtot = 80.4686 EPtot = -3526.0018 ! BOND = 14.0853 ANGLE = 81.3547 DIHED = 180.5432 ! 1-4 NB = 173.3468 1-4 EEL = 1409.4298 VDWAALS = -280.0634 ! EELEC = -2627.0632 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.6350 ------------------------------------------------------------------------------ ! Atomic Charges for Step 10 : Atom Element Mulliken Charge 1 N -0.470 2 H 0.237 *************** *** 588,602 **** 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 42.18 PRESS = 0.0 ! Etot = -3445.5332 EKtot = 80.4686 EPtot = -3526.0018 ! BOND = 14.0853 ANGLE = 81.3547 DIHED = 180.5432 ! 1-4 NB = 173.3468 1-4 EEL = 1409.4298 VDWAALS = -280.0634 ! EELEC = -2627.0632 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.6350 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 --- 624,638 ---- 24 H -0.089 Total Mulliken Charge = 0.000 ! NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 43.33 PRESS = 0.0 ! Etot = -3440.4103 EKtot = 82.6654 EPtot = -3523.0757 ! BOND = 17.2449 ANGLE = 85.5515 DIHED = 181.4093 ! 1-4 NB = 172.7192 1-4 EEL = 1404.8203 VDWAALS = -284.2430 ! EELEC = -2623.0761 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.5019 ------------------------------------------------------------------------------ ! Atomic Charges for Step 11 : Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 *************** *** 624,638 **** 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 11 TIME(PS) = 0.011 TEMP(K) = 43.33 PRESS = 0.0 ! Etot = -3440.4103 EKtot = 82.6654 EPtot = -3523.0757 ! BOND = 17.2449 ANGLE = 85.5515 DIHED = 181.4093 ! 1-4 NB = 172.7192 1-4 EEL = 1404.8203 VDWAALS = -284.2430 ! EELEC = -2623.0761 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.5019 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 --- 660,674 ---- 24 H -0.090 Total Mulliken Charge = 0.000 ! NSTEP = 12 TIME(PS) = 0.012 TEMP(K) = 44.96 PRESS = 0.0 ! Etot = -3451.0906 EKtot = 85.7647 EPtot = -3536.8554 ! BOND = 19.8228 ANGLE = 88.8158 DIHED = 182.6758 ! 1-4 NB = 171.9285 1-4 EEL = 1400.1874 VDWAALS = -288.0853 ! EELEC = -2634.5444 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.6559 ------------------------------------------------------------------------------ ! Atomic Charges for Step 12 : Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 *************** *** 660,674 **** 24 H -0.091 Total Mulliken Charge = 0.000 ! NSTEP = 12 TIME(PS) = 0.012 TEMP(K) = 44.96 PRESS = 0.0 ! Etot = -3451.0906 EKtot = 85.7647 EPtot = -3536.8554 ! BOND = 19.8228 ANGLE = 88.8158 DIHED = 182.6758 ! 1-4 NB = 171.9285 1-4 EEL = 1400.1874 VDWAALS = -288.0853 ! EELEC = -2634.5444 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.6559 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 --- 696,710 ---- 24 H -0.091 Total Mulliken Charge = 0.000 ! NSTEP = 13 TIME(PS) = 0.013 TEMP(K) = 47.85 PRESS = 0.0 ! Etot = -3474.4112 EKtot = 91.2799 EPtot = -3565.6911 ! BOND = 20.4428 ANGLE = 90.5874 DIHED = 184.3248 ! 1-4 NB = 170.9158 1-4 EEL = 1395.6402 VDWAALS = -291.5224 ! EELEC = -2658.3031 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.7767 ------------------------------------------------------------------------------ ! Atomic Charges for Step 13 : Atom Element Mulliken Charge 1 N -0.467 2 H 0.237 *************** *** 696,710 **** 24 H -0.092 Total Mulliken Charge = 0.000 ! NSTEP = 13 TIME(PS) = 0.013 TEMP(K) = 47.85 PRESS = 0.0 ! Etot = -3474.4112 EKtot = 91.2799 EPtot = -3565.6911 ! BOND = 20.4428 ANGLE = 90.5874 DIHED = 184.3248 ! 1-4 NB = 170.9158 1-4 EEL = 1395.6402 VDWAALS = -291.5224 ! EELEC = -2658.3031 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2477.7767 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.469 2 H 0.237 --- 732,746 ---- 24 H -0.092 Total Mulliken Charge = 0.000 ! NSTEP = 14 TIME(PS) = 0.014 TEMP(K) = 51.58 PRESS = 0.0 ! Etot = -3476.6948 EKtot = 98.3922 EPtot = -3575.0869 ! BOND = 20.4038 ANGLE = 90.7032 DIHED = 186.3178 ! 1-4 NB = 169.6802 1-4 EEL = 1391.3322 VDWAALS = -294.4995 ! EELEC = -2660.8569 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.1677 ------------------------------------------------------------------------------ ! Atomic Charges for Step 14 : Atom Element Mulliken Charge 1 N -0.469 2 H 0.237 *************** *** 732,746 **** 24 H -0.093 Total Mulliken Charge = 0.000 ! NSTEP = 14 TIME(PS) = 0.014 TEMP(K) = 51.58 PRESS = 0.0 ! Etot = -3476.6948 EKtot = 98.3922 EPtot = -3575.0869 ! BOND = 20.4038 ANGLE = 90.7032 DIHED = 186.3178 ! 1-4 NB = 169.6802 1-4 EEL = 1391.3322 VDWAALS = -294.4995 ! EELEC = -2660.8569 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2478.1677 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.471 2 H 0.237 --- 768,782 ---- 24 H -0.093 Total Mulliken Charge = 0.000 ! NSTEP = 15 TIME(PS) = 0.015 TEMP(K) = 54.99 PRESS = 0.0 ! Etot = -3472.1192 EKtot = 104.8977 EPtot = -3577.0169 ! BOND = 22.1014 ANGLE = 89.4225 DIHED = 188.6004 ! 1-4 NB = 168.2777 1-4 EEL = 1387.4242 VDWAALS = -296.9917 ! EELEC = -2656.6802 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2479.1711 ------------------------------------------------------------------------------ ! Atomic Charges for Step 15 : Atom Element Mulliken Charge 1 N -0.471 2 H 0.237 *************** *** 768,782 **** 24 H -0.094 Total Mulliken Charge = 0.000 ! NSTEP = 15 TIME(PS) = 0.015 TEMP(K) = 54.99 PRESS = 0.0 ! Etot = -3472.1192 EKtot = 104.8977 EPtot = -3577.0169 ! BOND = 22.1014 ANGLE = 89.4225 DIHED = 188.6004 ! 1-4 NB = 168.2777 1-4 EEL = 1387.4242 VDWAALS = -296.9917 ! EELEC = -2656.6802 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2479.1711 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.474 2 H 0.237 --- 804,818 ---- 24 H -0.094 Total Mulliken Charge = 0.000 ! NSTEP = 16 TIME(PS) = 0.016 TEMP(K) = 57.29 PRESS = 0.0 ! Etot = -3485.6965 EKtot = 109.2861 EPtot = -3594.9827 ! BOND = 26.2206 ANGLE = 87.3123 DIHED = 191.1084 ! 1-4 NB = 166.7997 1-4 EEL = 1384.0330 VDWAALS = -299.0181 ! EELEC = -2670.9924 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2480.4463 ------------------------------------------------------------------------------ ! Atomic Charges for Step 16 : Atom Element Mulliken Charge 1 N -0.474 2 H 0.237 *************** *** 804,818 **** 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 16 TIME(PS) = 0.016 TEMP(K) = 57.29 PRESS = 0.0 ! Etot = -3485.6965 EKtot = 109.2861 EPtot = -3594.9827 ! BOND = 26.2206 ANGLE = 87.3123 DIHED = 191.1084 ! 1-4 NB = 166.7997 1-4 EEL = 1384.0330 VDWAALS = -299.0181 ! EELEC = -2670.9924 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2480.4463 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.476 2 H 0.236 --- 840,854 ---- 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 17 TIME(PS) = 0.017 TEMP(K) = 58.71 PRESS = 0.0 ! Etot = -3486.3210 EKtot = 112.0092 EPtot = -3598.3302 ! BOND = 30.8062 ANGLE = 85.0429 DIHED = 193.7688 ! 1-4 NB = 165.3409 1-4 EEL = 1381.1850 VDWAALS = -300.6343 ! EELEC = -2672.6287 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2481.2109 ------------------------------------------------------------------------------ ! Atomic Charges for Step 17 : Atom Element Mulliken Charge 1 N -0.476 2 H 0.236 *************** *** 840,854 **** 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 17 TIME(PS) = 0.017 TEMP(K) = 58.71 PRESS = 0.0 ! Etot = -3486.3210 EKtot = 112.0092 EPtot = -3598.3302 ! BOND = 30.8062 ANGLE = 85.0429 DIHED = 193.7688 ! 1-4 NB = 165.3409 1-4 EEL = 1381.1850 VDWAALS = -300.6343 ! EELEC = -2672.6287 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2481.2109 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.478 2 H 0.236 --- 876,890 ---- 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 18 TIME(PS) = 0.018 TEMP(K) = 60.16 PRESS = 0.0 ! Etot = -3495.0511 EKtot = 114.7753 EPtot = -3609.8264 ! BOND = 33.1838 ANGLE = 83.1848 DIHED = 196.5015 ! 1-4 NB = 163.9709 1-4 EEL = 1378.8079 VDWAALS = -301.9213 ! EELEC = -2682.4570 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2481.0970 ------------------------------------------------------------------------------ ! Atomic Charges for Step 18 : Atom Element Mulliken Charge 1 N -0.478 2 H 0.236 *************** *** 876,890 **** 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 18 TIME(PS) = 0.018 TEMP(K) = 60.16 PRESS = 0.0 ! Etot = -3495.0511 EKtot = 114.7753 EPtot = -3609.8264 ! BOND = 33.1838 ANGLE = 83.1848 DIHED = 196.5015 ! 1-4 NB = 163.9709 1-4 EEL = 1378.8079 VDWAALS = -301.9213 ! EELEC = -2682.4570 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2481.0970 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.480 2 H 0.235 --- 912,926 ---- 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 19 TIME(PS) = 0.019 TEMP(K) = 62.21 PRESS = 0.0 ! Etot = -3486.0725 EKtot = 118.6717 EPtot = -3604.7442 ! BOND = 32.6065 ANGLE = 82.0953 DIHED = 199.2195 ! 1-4 NB = 162.7181 1-4 EEL = 1376.7439 VDWAALS = -302.9644 ! EELEC = -2674.3969 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2480.7661 ------------------------------------------------------------------------------ ! Atomic Charges for Step 19 : Atom Element Mulliken Charge 1 N -0.480 2 H 0.235 *************** *** 912,926 **** 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 19 TIME(PS) = 0.019 TEMP(K) = 62.21 PRESS = 0.0 ! Etot = -3486.0725 EKtot = 118.6717 EPtot = -3604.7442 ! BOND = 32.6065 ANGLE = 82.0953 DIHED = 199.2195 ! 1-4 NB = 162.7181 1-4 EEL = 1376.7439 VDWAALS = -302.9644 ! EELEC = -2674.3969 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2480.7661 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge 1 N -0.482 2 H 0.235 --- 948,962 ---- 24 H -0.095 Total Mulliken Charge = 0.000 ! NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 64.37 PRESS = 0.0 ! Etot = -3473.8493 EKtot = 122.8009 EPtot = -3596.6502 ! BOND = 30.8156 ANGLE = 81.8978 DIHED = 201.8349 ! 1-4 NB = 161.5665 1-4 EEL = 1374.7956 VDWAALS = -303.8431 ! EELEC = -2662.7999 EHBOND = 0.0000 RESTRAINT = 0.0000 ! DFTBESCF= -2480.9175 ------------------------------------------------------------------------------ ! Atomic Charges for Step 20 : Atom Element Mulliken Charge 1 N -0.482 2 H 0.235 *************** *** 948,962 **** 24 H -0.095 Total Mulliken Charge = 0.000 - NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 64.37 PRESS = 0.0 - Etot = -3473.8493 EKtot = 122.8009 EPtot = -3596.6502 - BOND = 30.8156 ANGLE = 81.8978 DIHED = 201.8349 - 1-4 NB = 161.5665 1-4 EEL = 1374.7956 VDWAALS = -303.8431 - EELEC = -2662.7999 EHBOND = 0.0000 RESTRAINT = 0.0000 - DFTBESCF= -2480.9175 - ------------------------------------------------------------------------------ - - A V E R A G E S O V E R 20 S T E P S --- 984,989 ---- *************** *** 985,1023 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.02% of Total) ! | Build the list 0.01 (93.79% of List ) ! | Other 0.00 ( 6.21% of List ) ! | List time 0.01 ( 5.43% of Nonbo) ! | Short_ene time 0.19 (99.58% of Direc) ! | Other 0.00 ( 0.42% of Direc) ! | Direct Ewald time 0.19 (98.33% of Ewald) ! | Force Adjust 0.00 ( 1.55% of Ewald) ! | Virial junk 0.00 ( 0.03% of Ewald) ! | Start sycnronization 0.00 ( 0.02% of Ewald) ! | Other 0.00 ( 0.08% of Ewald) ! | Ewald time 0.20 (94.52% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Other 0.00 ( 0.04% of Nonbo) ! | Nonbond force 0.21 ( 1.37% of Force) ! | QMMM setup 0.18 ( 1.19% of QMMM ) ! | QMMM list build 0.00 ( 0.01% of QMMM ) ! | QMMM scf 14.80 (100.0% of QMMM ) ! | QMMM energy 14.80 (98.74% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.01% of QMMM ) ! | QMMM Mulliken Chgs 0.01 ( 0.05% of QMMM ) ! | QMMM 14.99 (98.50% of Force) ! | Bond/Angle/Dihedral 0.02 ( 0.13% of Force) ! | Force time 15.22 (99.56% of Runmd) ! | Verlet update time 0.06 ( 0.41% of Runmd) ! | Other 0.00 ( 0.03% of Runmd) ! | Runmd Time 15.28 (99.80% of Total) ! | Other 0.03 ( 0.18% of Total) ! | Total time 15.31 (100.0% of ALL ) | Highest rstack allocated: 2400 | Highest istack allocated: 480 ! | Job began at 10:20:54.717 on 03/13/2006 ! | Setup done at 10:20:54.747 on 03/13/2006 ! | Run done at 10:21:10.031 on 03/13/2006 ! | wallclock() was called 1138 times --- 1012,1055 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.11% of Total) ! | Build the list 0.01 (95.22% of List ) ! | Other 0.00 ( 4.78% of List ) ! | List time 0.01 ( 3.81% of Nonbo) ! | Short_ene time 0.21 (99.80% of Direc) ! | Other 0.00 ( 0.20% of Direc) ! | Direct Ewald time 0.21 (98.45% of Ewald) ! | Force Adjust 0.00 ( 1.50% of Ewald) ! | Virial junk 0.00 ( 0.01% of Ewald) ! | Start sycnronization 0.00 ( 0.01% of Ewald) ! | Other 0.00 ( 0.03% of Ewald) ! | Ewald time 0.21 (96.16% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Other 0.00 ( 0.02% of Nonbo) ! | Nonbond force 0.22 (17.78% of Force) ! | QMMM setup 0.12 (11.98% of QMMM ) ! | QMMM list build 0.00 ( 0.08% of QMMM ) ! | QMMM prep coords 0.00 ( 0.03% of QMMM ) ! | QMMM scf 0.88 (100.0% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM energy 0.89 (87.85% of QMMM ) ! | QMMM QM-QM force 0.00 ( 0.01% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.03% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.02% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM 1.01 (80.68% of Force) ! | Bond/Angle/Dihedral 0.02 ( 1.53% of Force) ! | Other 0.00 ( 0.01% of Force) ! | Force time 1.25 (98.99% of Runmd) ! | Verlet update time 0.01 ( 0.96% of Runmd) ! | Other 0.00 ( 0.05% of Runmd) ! | Runmd Time 1.26 (98.62% of Total) ! | Other 0.02 ( 1.27% of Total) ! | Total time 1.28 (100.0% of ALL ) | Highest rstack allocated: 2400 | Highest istack allocated: 480 ! | Job began at 14:11:33.933 on 04/17/2007 ! | Setup done at 14:11:33.951 on 04/17/2007 ! | Run done at 14:11:35.213 on 04/17/2007 ! | wallclock() was called 1100 times *** test/qmmm_DFTB/crambin_DFTB/crambin_md_hot_start.out.save 2006-04-03 18:15:18.000000000 -0700 --- test/qmmm_DFTB/crambin_DFTB/crambin_md_hot_start.out.save 2007-04-17 14:11:56.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:40:44 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:24 [-O]verwriting output File Assignments: *************** *** 141,147 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information --- 141,147 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information *************** *** 168,189 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9/serial/dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9/serial/dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9/serial/dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9/serial/dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9/serial/dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9/serial/dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9/serial/dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 168,189 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 393,420 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.01% of Total) ! | Calc gb off-diag 0.08 (97.98% of Gen B) ! | Other 0.00 ( 2.02% of Gen B) ! | Gen Born time 0.08 (100.0% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Nonbond force 0.08 ( 0.31% of Force) ! | QMMM setup 0.11 ( 0.41% of QMMM ) ! | QMMM scf 25.74 (100.0% of QMMM ) ! | QMMM GB energy 0.00 ( 0.01% of QMMM ) ! | QMMM energy 25.74 (99.58% of QMMM ) ! | QMMM 25.85 (99.66% of Force) ! | Bond/Angle/Dihedral 0.01 ( 0.03% of Force) ! | Force time 25.94 (99.90% of Runmd) ! | Verlet update time 0.02 ( 0.09% of Runmd) ! | Other 0.00 ( 0.01% of Runmd) ! | Runmd Time 25.97 (99.88% of Total) ! | Other 0.03 ( 0.11% of Total) ! | Total time 26.00 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 10:40:44.457 on 03/13/2006 ! | Setup done at 10:40:44.489 on 03/13/2006 ! | Run done at 10:41:10.457 on 03/13/2006 | wallclock() was called 294 times --- 393,422 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.06% of Total) ! | Calc gb off-diag 0.06 (97.74% of Gen B) ! | Other 0.00 ( 2.26% of Gen B) ! | Gen Born time 0.06 (100.0% of Nonbo) | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Nonbond force 0.06 ( 2.11% of Force) ! | QMMM setup 0.07 ( 2.70% of QMMM ) ! | QMMM list build 0.00 ( 0.02% of QMMM ) ! | QMMM prep coords 0.00 ( 0.01% of QMMM ) ! | QMMM scf 2.62 (100.0% of QMMM ) ! | QMMM GB energy 0.00 ( 0.05% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.62 (97.26% of QMMM ) ! | QMMM 2.70 (97.68% of Force) ! | Bond/Angle/Dihedral 0.01 ( 0.22% of Force) ! | Force time 2.76 (99.35% of Runmd) ! | Verlet update time 0.02 ( 0.65% of Runmd) ! | Runmd Time 2.78 (99.27% of Total) ! | Other 0.02 ( 0.67% of Total) ! | Total time 2.80 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:11:24.852 on 04/17/2007 ! | Setup done at 14:11:24.873 on 04/17/2007 ! | Run done at 14:11:27.650 on 04/17/2007 | wallclock() was called 294 times *** test/qmmm_DFTB/crambin_DFTB/crambin_md.out.save 2006-04-03 18:15:18.000000000 -0700 --- test/qmmm_DFTB/crambin_DFTB/crambin_md.out.save 2007-04-17 14:11:46.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:39:05 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:27 [-O]verwriting output File Assignments: *************** *** 136,142 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information --- 136,142 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information *************** *** 163,184 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9/serial/dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9/serial/dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9/serial/dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9/serial/dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9/serial/dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9/serial/dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9/serial/dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 163,184 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 389,415 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.01% of Total) ! | Calc gb off-diag 0.03 (96.41% of Gen B) ! | Other 0.00 ( 3.59% of Gen B) | Gen Born time 0.03 (100.0% of Nonbo) ! | IPS excludes 0.00 ( 0.02% of Nonbo) ! | Nonbond force 0.03 ( 0.13% of Force) ! | QMMM setup 0.10 ( 0.40% of QMMM ) ! | QMMM scf 26.33 (100.0% of QMMM ) ! | QMMM energy 26.33 (99.60% of QMMM ) ! | QMMM 26.44 (99.84% of Force) ! | Bond/Angle/Dihedral 0.01 ( 0.02% of Force) ! | Force time 26.48 (99.87% of Runmd) ! | Verlet update time 0.03 ( 0.12% of Runmd) ! | Other 0.00 ( 0.01% of Runmd) ! | Runmd Time 26.51 (99.88% of Total) ! | Other 0.03 ( 0.11% of Total) ! | Total time 26.54 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 10:39:05.828 on 03/13/2006 ! | Setup done at 10:39:05.859 on 03/13/2006 ! | Run done at 10:39:32.373 on 03/13/2006 | wallclock() was called 294 times --- 389,418 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.05% of Total) ! | Calc gb off-diag 0.03 (96.67% of Gen B) ! | Other 0.00 ( 3.33% of Gen B) | Gen Born time 0.03 (100.0% of Nonbo) ! | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Nonbond force 0.03 ( 0.94% of Force) ! | QMMM setup 0.07 ( 2.64% of QMMM ) ! | QMMM list build 0.00 ( 0.04% of QMMM ) ! | QMMM prep coords 0.00 ( 0.01% of QMMM ) ! | QMMM scf 2.70 (100.0% of QMMM ) ! | QMMM GB energy 0.00 ( 0.03% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.70 (97.30% of QMMM ) ! | QMMM 2.77 (98.84% of Force) ! | Bond/Angle/Dihedral 0.01 ( 0.21% of Force) ! | Force time 2.80 (98.97% of Runmd) ! | Verlet update time 0.03 ( 1.03% of Runmd) ! | Runmd Time 2.83 (99.30% of Total) ! | Other 0.02 ( 0.65% of Total) ! | Total time 2.85 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:11:27.782 on 04/17/2007 ! | Setup done at 14:11:27.802 on 04/17/2007 ! | Run done at 14:11:30.635 on 04/17/2007 | wallclock() was called 294 times *** test/qmmm_DFTB/crambin_DFTB/crambin.out.save 2006-04-03 18:15:18.000000000 -0700 --- test/qmmm_DFTB/crambin_DFTB/crambin.out.save 2007-04-17 14:11:40.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:24:11 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:22 [-O]verwriting output File Assignments: *************** *** 136,142 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information --- 136,142 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 0.916 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- QMMM: Link Atom Information *************** *** 163,184 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9/serial/dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9/serial/dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9/serial/dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9/serial/dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9/serial/dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9/serial/dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9/serial/dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 163,184 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 1 (c ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/co.spl ! | 5 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 6 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 7 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 8 2 (h ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/ho.spl ! | 9 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 10 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 11 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl ! | 12 3 (n ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/no.spl ! | 13 4 (o ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/oc.spl ! | 14 4 (o ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/oh.spl ! | 15 4 (o ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/on.spl ! | 16 4 (o ) 4 (o ) /usr/local/amber9_release/amber9_new//dat/slko/oo.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 371,395 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.01% of Total) ! | Calc gb off-diag 0.03 (96.41% of Gen B) ! | Other 0.00 ( 3.59% of Gen B) ! | Gen Born time 0.03 (100.0% of Nonbo) ! | IPS excludes 0.00 ( 0.02% of Nonbo) ! | Nonbond force 0.03 ( 0.14% of Force) ! | QMMM setup 0.11 ( 0.54% of QMMM ) ! | QMMM scf 20.34 (100.0% of QMMM ) ! | QMMM energy 20.34 (99.45% of QMMM ) ! | QMMM 20.45 (99.83% of Force) ! | Bond/Angle/Dihedral 0.01 ( 0.03% of Force) ! | Force time 20.49 (100.0% of Runmd) ! | Runmd Time 20.49 (99.69% of Total) ! | Other 0.06 ( 0.29% of Total) ! | Total time 20.55 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 10:24:11.991 on 03/13/2006 ! | Setup done at 10:24:12.034 on 03/13/2006 ! | Run done at 10:24:32.541 on 03/13/2006 | wallclock() was called 228 times --- 371,399 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.06% of Total) ! | Calc gb off-diag 0.02 (96.75% of Gen B) ! | Other 0.00 ( 3.25% of Gen B) ! | Gen Born time 0.02 (100.0% of Nonbo) ! | IPS excludes 0.00 ( 0.01% of Nonbo) ! | Nonbond force 0.02 ( 1.03% of Force) ! | QMMM setup 0.07 ( 3.39% of QMMM ) ! | QMMM list build 0.00 ( 0.05% of QMMM ) ! | QMMM prep coords 0.00 ( 0.01% of QMMM ) ! | QMMM scf 2.02 (100.0% of QMMM ) ! | QMMM GB energy 0.00 ( 0.03% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM energy 2.02 (96.55% of QMMM ) ! | QMMM 2.09 (98.73% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.23% of Force) ! | Force time 2.12 (100.0% of Runmd) ! | Runmd Time 2.12 (98.94% of Total) ! | Other 0.02 ( 0.99% of Total) ! | Total time 2.14 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:11:22.575 on 04/17/2007 ! | Setup done at 14:11:22.595 on 04/17/2007 ! | Run done at 14:11:24.720 on 04/17/2007 | wallclock() was called 228 times *** test/qmmm_DFTB/lysine_DFTB_calc_mulliken/lysine_md.out.save 2006-04-03 18:15:22.000000000 -0700 --- test/qmmm_DFTB/lysine_DFTB_calc_mulliken/lysine_md.out.save 2007-04-17 14:11:08.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:43:30 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:10:32 [-O]verwriting output File Assignments: *************** *** 151,160 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 4 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 151,160 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 4 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 207,219 **** DFTBESCF= -437.1852 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.323 ! 2 H 0.092 ! 3 H 0.100 ! 4 H 0.114 ! 5 H 0.017 Total Mulliken Charge = 0.000 NSTEP = 2 TIME(PS) = 0.402 TEMP(K) = 358.98 PRESS = 0.0 --- 207,219 ---- DFTBESCF= -437.1852 ------------------------------------------------------------------------------ ! Atomic Charges for Step 1 : Atom Element Mulliken Charge ! 1 C -0.328 ! 2 H 0.095 ! 3 H 0.102 ! 4 H 0.116 ! 5 H 0.014 Total Mulliken Charge = 0.000 NSTEP = 2 TIME(PS) = 0.402 TEMP(K) = 358.98 PRESS = 0.0 *************** *** 224,236 **** DFTBESCF= -438.1630 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.318 ! 2 H 0.087 ! 3 H 0.098 ! 4 H 0.112 ! 5 H 0.020 Total Mulliken Charge = 0.000 NSTEP = 3 TIME(PS) = 0.403 TEMP(K) = 342.31 PRESS = 0.0 --- 224,236 ---- DFTBESCF= -438.1630 ------------------------------------------------------------------------------ ! Atomic Charges for Step 2 : Atom Element Mulliken Charge ! 1 C -0.323 ! 2 H 0.092 ! 3 H 0.100 ! 4 H 0.114 ! 5 H 0.017 Total Mulliken Charge = 0.000 NSTEP = 3 TIME(PS) = 0.403 TEMP(K) = 342.31 PRESS = 0.0 *************** *** 241,253 **** DFTBESCF= -438.0946 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.313 ! 2 H 0.082 ! 3 H 0.097 ! 4 H 0.111 ! 5 H 0.024 Total Mulliken Charge = 0.000 NSTEP = 4 TIME(PS) = 0.404 TEMP(K) = 308.18 PRESS = 0.0 --- 241,253 ---- DFTBESCF= -438.0946 ------------------------------------------------------------------------------ ! Atomic Charges for Step 3 : Atom Element Mulliken Charge ! 1 C -0.318 ! 2 H 0.087 ! 3 H 0.098 ! 4 H 0.112 ! 5 H 0.020 Total Mulliken Charge = 0.000 NSTEP = 4 TIME(PS) = 0.404 TEMP(K) = 308.18 PRESS = 0.0 *************** *** 258,270 **** DFTBESCF= -437.0349 ------------------------------------------------------------------------------ ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.311 ! 2 H 0.078 ! 3 H 0.096 ! 4 H 0.110 ! 5 H 0.027 Total Mulliken Charge = 0.000 NSTEP = 5 TIME(PS) = 0.405 TEMP(K) = 297.20 PRESS = 0.0 --- 258,270 ---- DFTBESCF= -437.0349 ------------------------------------------------------------------------------ ! Atomic Charges for Step 4 : Atom Element Mulliken Charge ! 1 C -0.313 ! 2 H 0.082 ! 3 H 0.097 ! 4 H 0.111 ! 5 H 0.024 Total Mulliken Charge = 0.000 NSTEP = 5 TIME(PS) = 0.405 TEMP(K) = 297.20 PRESS = 0.0 *************** *** 275,280 **** --- 275,288 ---- DFTBESCF= -436.0651 ------------------------------------------------------------------------------ + Atomic Charges for Step 5 : + Atom Element Mulliken Charge + 1 C -0.311 + 2 H 0.078 + 3 H 0.096 + 4 H 0.110 + 5 H 0.027 + Total Mulliken Charge = 0.000 A V E R A G E S O V E R 5 S T E P S *************** *** 305,343 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.52% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Calc gb off-diag 0.00 (75.37% of Gen B) ! | Other 0.00 (24.63% of Gen B) ! | Gen Born time 0.00 (97.92% of Nonbo) ! | IPS excludes 0.00 ( 2.08% of Nonbo) ! | Nonbond force 0.00 ( 0.54% of Force) ! | QMMM setup 0.02 (45.09% of QMMM ) ! | QMMM list build 0.00 ( 0.04% of QMMM ) ! | QMMM prep coords 0.00 ( 0.25% of QMMM ) | QMMM RIJ Eqns Calc 0.00 ( 0.02% of QMMM ) ! | QMMM scf 0.03 (99.82% of QMMM ) ! | QMMM GB energy 0.00 ( 0.06% of QMMM ) ! | Other 0.00 ( 0.13% of QMMM ) ! | QMMM energy 0.03 (53.45% of QMMM ) | QMMM QM-QM force 0.00 ( 0.04% of QMMM ) | QMMM QM-MM force 0.00 ( 0.05% of QMMM ) ! | QMMM Mulliken Chgs 0.00 ( 0.89% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.05% of QMMM ) ! | Other 0.00 ( 0.11% of QMMM ) ! | QMMM 0.05 (98.67% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.78% of Force) ! | Other 0.00 ( 0.01% of Force) ! | Force time 0.05 (81.04% of Runmd) ! | Verlet update time 0.01 (15.60% of Runmd) ! | Other 0.00 ( 3.36% of Runmd) ! | Runmd Time 0.07 (87.12% of Total) ! | Other 0.01 (12.34% of Total) ! | Total time 0.08 (99.83% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 10:43:30.706 on 03/13/2006 ! | Setup done at 10:43:30.716 on 03/13/2006 ! | Run done at 10:43:30.782 on 03/13/2006 ! | wallclock() was called 258 times --- 313,349 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.95% of Total) ! | Fast Water setup 0.00 ( 0.03% of Total) ! | Calc gb off-diag 0.00 (74.70% of Gen B) ! | Other 0.00 (25.30% of Gen B) ! | Gen Born time 0.00 (98.87% of Nonbo) ! | IPS excludes 0.00 ( 1.13% of Nonbo) ! | Nonbond force 0.00 ( 0.85% of Force) ! | QMMM setup 0.02 (80.66% of QMMM ) ! | QMMM list build 0.00 ( 0.07% of QMMM ) ! | QMMM prep coords 0.00 ( 0.30% of QMMM ) | QMMM RIJ Eqns Calc 0.00 ( 0.02% of QMMM ) ! | QMMM scf 0.00 (99.15% of QMMM ) ! | QMMM GB energy 0.00 ( 0.32% of QMMM ) ! | Other 0.00 ( 0.53% of QMMM ) ! | QMMM energy 0.00 (18.63% of QMMM ) | QMMM QM-QM force 0.00 ( 0.04% of QMMM ) | QMMM QM-MM force 0.00 ( 0.05% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.08% of QMMM ) ! | Other 0.00 ( 0.14% of QMMM ) ! | QMMM 0.02 (97.99% of Force) ! | Bond/Angle/Dihedral 0.00 ( 1.16% of Force) ! | Force time 0.02 (93.55% of Runmd) ! | Verlet update time 0.00 ( 5.53% of Runmd) ! | Other 0.00 ( 0.92% of Runmd) ! | Runmd Time 0.02 (88.75% of Total) ! | Other 0.00 (10.27% of Total) ! | Total time 0.02 (99.68% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:10:32.704 on 04/17/2007 ! | Setup done at 14:10:32.707 on 04/17/2007 ! | Run done at 14:10:32.730 on 04/17/2007 ! | wallclock() was called 250 times *** test/qmmm_DFTB/lysine_DFTB_calc_mulliken/lysine.out.save 2006-04-03 18:15:22.000000000 -0700 --- test/qmmm_DFTB/lysine_DFTB_calc_mulliken/lysine.out.save 2007-04-17 14:10:59.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:43:29 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:10:32 [-O]verwriting output File Assignments: *************** *** 149,158 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 4 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 149,158 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 4 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 196,209 **** 4. RESULTS -------------------------------------------------------------------------------- - Atomic Charges: - Atom Element Mulliken Charge - 1 C -0.317 - 2 H 0.076 - 3 H 0.099 - 4 H 0.120 - 5 H 0.022 - Total Mulliken Charge = 0.000 NSTEP ENERGY RMS GMAX NAME NUMBER --- 196,201 ---- *************** *** 213,225 **** VDWAALS = 0.1908 EEL = -4.8553 EGB = 0.0000 1-4 VDW = 3.7051 1-4 EEL = 65.4625 RESTRAINT = 0.0000 DFTBESCF= -438.7307 ! Atomic Charges: Atom Element Mulliken Charge ! 1 C -0.316 2 H 0.076 3 H 0.099 ! 4 H 0.121 ! 5 H 0.021 Total Mulliken Charge = 0.000 --- 205,217 ---- VDWAALS = 0.1908 EEL = -4.8553 EGB = 0.0000 1-4 VDW = 3.7051 1-4 EEL = 65.4625 RESTRAINT = 0.0000 DFTBESCF= -438.7307 ! Atomic Charges for Step 1 : Atom Element Mulliken Charge ! 1 C -0.317 2 H 0.076 3 H 0.099 ! 4 H 0.120 ! 5 H 0.022 Total Mulliken Charge = 0.000 *************** *** 230,236 **** VDWAALS = 0.1283 EEL = -4.9209 EGB = 0.0000 1-4 VDW = 3.6106 1-4 EEL = 65.3800 RESTRAINT = 0.0000 DFTBESCF= -438.7387 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 --- 222,228 ---- VDWAALS = 0.1283 EEL = -4.9209 EGB = 0.0000 1-4 VDW = 3.6106 1-4 EEL = 65.3800 RESTRAINT = 0.0000 DFTBESCF= -438.7387 ! Atomic Charges for Step 2 : Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 *************** *** 247,258 **** VDWAALS = 0.0586 EEL = -4.9703 EGB = 0.0000 1-4 VDW = 3.5005 1-4 EEL = 65.2679 RESTRAINT = 0.0000 DFTBESCF= -438.7464 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 3 H 0.099 ! 4 H 0.122 5 H 0.021 Total Mulliken Charge = 0.000 --- 239,250 ---- VDWAALS = 0.0586 EEL = -4.9703 EGB = 0.0000 1-4 VDW = 3.5005 1-4 EEL = 65.2679 RESTRAINT = 0.0000 DFTBESCF= -438.7464 ! Atomic Charges for Step 3 : Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 3 H 0.099 ! 4 H 0.121 5 H 0.021 Total Mulliken Charge = 0.000 *************** *** 264,276 **** VDWAALS = -0.0166 EEL = -5.0010 EGB = 0.0000 1-4 VDW = 3.3898 1-4 EEL = 65.1611 RESTRAINT = 0.0000 DFTBESCF= -438.7512 ! Atomic Charges: Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 ! 3 H 0.098 4 H 0.122 ! 5 H 0.020 Total Mulliken Charge = 0.000 --- 256,268 ---- VDWAALS = -0.0166 EEL = -5.0010 EGB = 0.0000 1-4 VDW = 3.3898 1-4 EEL = 65.1611 RESTRAINT = 0.0000 DFTBESCF= -438.7512 ! Atomic Charges for Step 4 : Atom Element Mulliken Charge 1 C -0.316 2 H 0.076 ! 3 H 0.099 4 H 0.122 ! 5 H 0.021 Total Mulliken Charge = 0.000 *************** *** 281,286 **** --- 273,286 ---- VDWAALS = -0.1080 EEL = -5.0520 EGB = 0.0000 1-4 VDW = 3.2650 1-4 EEL = 65.0614 RESTRAINT = 0.0000 DFTBESCF= -438.7544 + Atomic Charges for Step 5 : + Atom Element Mulliken Charge + 1 C -0.316 + 2 H 0.076 + 3 H 0.098 + 4 H 0.122 + 5 H 0.020 + Total Mulliken Charge = 0.000 Maximum number of minimization cycles reached. *************** *** 302,338 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 0.66% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Calc gb off-diag 0.00 (76.09% of Gen B) ! | Other 0.00 (23.91% of Gen B) ! | Gen Born time 0.00 (98.02% of Nonbo) ! | IPS excludes 0.00 ( 1.98% of Nonbo) ! | Nonbond force 0.00 ( 0.60% of Force) ! | QMMM setup 0.03 (50.77% of QMMM ) ! | QMMM list build 0.00 ( 0.04% of QMMM ) ! | QMMM prep coords 0.00 ( 0.27% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 0.02% of QMMM ) ! | QMMM scf 0.02 (99.78% of QMMM ) ! | QMMM GB energy 0.00 ( 0.08% of QMMM ) ! | Other 0.00 ( 0.14% of QMMM ) ! | QMMM energy 0.02 (47.43% of QMMM ) ! | QMMM QM-QM force 0.00 ( 0.04% of QMMM ) | QMMM QM-MM force 0.00 ( 0.05% of QMMM ) ! | QMMM Mulliken Chgs 0.00 ( 1.21% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.06% of QMMM ) ! | Other 0.00 ( 0.10% of QMMM ) ! | QMMM 0.05 (98.58% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.80% of Force) ! | Other 0.00 ( 0.02% of Force) ! | Force time 0.05 (100.0% of Runmd) ! | Runmd Time 0.05 (72.69% of Total) ! | Other 0.02 (26.63% of Total) ! | Total time 0.07 (99.81% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 10:43:29.154 on 03/13/2006 ! | Setup done at 10:43:29.163 on 03/13/2006 ! | Run done at 10:43:29.223 on 03/13/2006 ! | wallclock() was called 238 times --- 302,337 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.00 ( 1.46% of Total) ! | Fast Water setup 0.00 ( 0.03% of Total) ! | Calc gb off-diag 0.00 (75.12% of Gen B) ! | Other 0.00 (24.88% of Gen B) ! | Gen Born time 0.00 (98.23% of Nonbo) ! | IPS excludes 0.00 ( 1.77% of Nonbo) ! | Nonbond force 0.00 ( 0.84% of Force) ! | QMMM setup 0.02 (83.20% of QMMM ) ! | QMMM list build 0.00 ( 0.08% of QMMM ) ! | QMMM prep coords 0.00 ( 0.31% of QMMM ) ! | QMMM RIJ Eqns Calc 0.00 ( 0.03% of QMMM ) ! | QMMM scf 0.00 (99.10% of QMMM ) ! | QMMM GB energy 0.00 ( 0.34% of QMMM ) ! | Other 0.00 ( 0.56% of QMMM ) ! | QMMM energy 0.00 (16.10% of QMMM ) ! | QMMM QM-QM force 0.00 ( 0.05% of QMMM ) | QMMM QM-MM force 0.00 ( 0.05% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.08% of QMMM ) ! | Other 0.00 ( 0.11% of QMMM ) ! | QMMM 0.02 (97.95% of Force) ! | Bond/Angle/Dihedral 0.00 ( 1.19% of Force) ! | Other 0.00 ( 0.01% of Force) ! | Force time 0.02 (100.0% of Runmd) ! | Runmd Time 0.02 (82.43% of Total) ! | Other 0.00 (16.07% of Total) ! | Total time 0.02 (99.68% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 14:10:32.589 on 04/17/2007 ! | Setup done at 14:10:32.593 on 04/17/2007 ! | Run done at 14:10:32.614 on 04/17/2007 ! | wallclock() was called 228 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.imaged_md.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.imaged_md.save 2007-04-17 14:13:41.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:44:28 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:38 [-O]verwriting output File Assignments: *************** *** 158,164 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 158,164 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 183,197 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 183,197 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 408,443 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.11% of Total) ! | Build the list 0.62 (98.69% of List ) ! | Other 0.01 ( 1.31% of List ) ! | List time 0.63 (13.48% of Nonbo) ! | Short_ene time 4.01 (98.95% of Direc) ! | Other 0.04 ( 1.05% of Direc) ! | Direct Ewald time 4.06 (99.90% of Ewald) ! | Force Adjust 0.00 ( 0.05% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 4.06 (86.52% of Nonbo) ! | Nonbond force 4.69 (14.10% of Force) ! | QMMM setup 0.06 ( 0.20% of QMMM ) ! | QMMM list build 0.01 ( 0.04% of QMMM ) ! | QMMM prep coords 0.01 ( 0.04% of QMMM ) ! | QMMM scf 28.51 (100.0% of QMMM ) ! | QMMM energy 28.51 (99.69% of QMMM ) ! | QMMM QM-MM force 0.01 ( 0.02% of QMMM ) ! | QMMM 28.60 (85.89% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 33.29 (99.17% of Runmd) ! | Shake time 0.02 ( 0.07% of Runmd) ! | Verlet update time 0.25 ( 0.74% of Runmd) ! | Other 0.01 ( 0.02% of Runmd) ! | Runmd Time 33.57 (99.33% of Total) ! | Other 0.19 ( 0.56% of Total) ! | Total time 33.80 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 10:44:28.527 on 03/13/2006 ! | Setup done at 10:44:28.754 on 03/13/2006 ! | Run done at 10:45:02.326 on 03/13/2006 | wallclock() was called 600 times --- 408,446 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.35% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.59 (99.32% of List ) ! | Other 0.00 ( 0.68% of List ) ! | List time 0.59 (13.54% of Nonbo) ! | Short_ene time 3.76 (99.35% of Direc) ! | Other 0.02 ( 0.65% of Direc) ! | Direct Ewald time 3.78 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.02% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 3.79 (86.46% of Nonbo) ! | Nonbond force 4.38 (65.80% of Force) ! | QMMM setup 0.04 ( 1.76% of QMMM ) ! | QMMM list build 0.01 ( 0.45% of QMMM ) ! | QMMM prep coords 0.01 ( 0.35% of QMMM ) ! | QMMM scf 2.21 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.21 (97.32% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.08% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 2.28 (34.19% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 6.66 (98.46% of Runmd) ! | Shake time 0.02 ( 0.22% of Runmd) ! | Verlet update time 0.09 ( 1.29% of Runmd) ! | Other 0.00 ( 0.02% of Runmd) ! | Runmd Time 6.76 (97.65% of Total) ! | Other 0.14 ( 1.99% of Total) ! | Total time 6.92 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 14:12:38.800 on 04/17/2007 ! | Setup done at 14:12:38.962 on 04/17/2007 ! | Run done at 14:12:45.723 on 04/17/2007 | wallclock() was called 600 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.imaged.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.imaged.save 2007-04-17 14:13:33.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:44:11 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:35 [-O]verwriting output File Assignments: *************** *** 148,154 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 148,154 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 173,187 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 173,187 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 336,370 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.03 ( 0.23% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.65 (99.16% of List ) ! | Other 0.01 ( 0.84% of List ) ! | List time 0.65 (26.01% of Nonbo) ! | Short_ene time 1.84 (98.96% of Direc) ! | Other 0.02 ( 1.04% of Direc) ! | Direct Ewald time 1.86 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.86 (73.99% of Nonbo) ! | Nonbond force 2.51 (18.88% of Force) ! | QMMM setup 0.06 ( 0.54% of QMMM ) ! | QMMM list build 0.01 ( 0.06% of QMMM ) ! | QMMM prep coords 0.01 ( 0.05% of QMMM ) ! | QMMM scf 10.73 (100.0% of QMMM ) ! | QMMM energy 10.73 (99.31% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.04% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 10.80 (81.09% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.03% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 13.32 (100.0% of Runmd) ! | Runmd Time 13.32 (97.21% of Total) ! | Other 0.35 ( 2.56% of Total) ! | Total time 13.70 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 10:44:11.012 on 03/13/2006 ! | Setup done at 10:44:11.257 on 03/13/2006 ! | Run done at 10:44:24.716 on 03/13/2006 | wallclock() was called 250 times --- 336,371 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.50% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Build the list 0.58 (99.50% of List ) ! | Other 0.00 ( 0.50% of List ) ! | List time 0.58 (25.60% of Nonbo) ! | Short_ene time 1.68 (99.36% of Direc) ! | Other 0.01 ( 0.64% of Direc) ! | Direct Ewald time 1.69 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.69 (74.40% of Nonbo) ! | Nonbond force 2.27 (71.85% of Force) ! | QMMM setup 0.04 ( 4.40% of QMMM ) ! | QMMM list build 0.00 ( 0.52% of QMMM ) ! | QMMM prep coords 0.00 ( 0.42% of QMMM ) ! | QMMM scf 0.84 (100.0% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM energy 0.84 (94.52% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.10% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.04% of QMMM ) ! | QMMM 0.89 (28.06% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.08% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 3.16 (100.0% of Runmd) ! | Runmd Time 3.16 (93.55% of Total) ! | Other 0.20 ( 5.93% of Total) ! | Total time 3.38 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 14:12:35.278 on 04/17/2007 ! | Setup done at 14:12:35.449 on 04/17/2007 ! | Run done at 14:12:38.658 on 04/17/2007 | wallclock() was called 250 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center_bigqmcut_md.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center_bigqmcut_md.save 2007-04-17 14:14:03.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:46:49 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:56 [-O]verwriting output File Assignments: *************** *** 159,165 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 159,165 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 184,198 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 184,198 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 409,445 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.12% of Total) ! | Build the list 0.66 (98.81% of List ) ! | Other 0.01 ( 1.19% of List ) ! | List time 0.67 (14.24% of Nonbo) ! | Short_ene time 4.00 (98.92% of Direc) ! | Other 0.04 ( 1.08% of Direc) ! | Direct Ewald time 4.05 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.05% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 4.05 (85.76% of Nonbo) ! | Nonbond force 4.72 (14.81% of Force) ! | QMMM setup 0.06 ( 0.22% of QMMM ) ! | QMMM list build 0.02 ( 0.07% of QMMM ) ! | QMMM prep coords 0.01 ( 0.05% of QMMM ) ! | QMMM scf 27.07 (100.0% of QMMM ) ! | QMMM energy 27.07 (99.62% of QMMM ) ! | QMMM QM-MM force 0.01 ( 0.03% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 27.18 (85.18% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 31.90 (99.13% of Runmd) ! | Shake time 0.02 ( 0.07% of Runmd) ! | Verlet update time 0.25 ( 0.78% of Runmd) ! | Other 0.01 ( 0.02% of Runmd) ! | Runmd Time 32.18 (99.31% of Total) ! | Other 0.19 ( 0.57% of Total) ! | Total time 32.41 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 10:46:49.190 on 03/13/2006 ! | Setup done at 10:46:49.414 on 03/13/2006 ! | Run done at 10:47:21.597 on 03/13/2006 | wallclock() was called 600 times --- 409,447 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.34% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.63 (99.37% of List ) ! | Other 0.00 ( 0.63% of List ) ! | List time 0.64 (14.49% of Nonbo) ! | Short_ene time 3.74 (99.34% of Direc) ! | Other 0.02 ( 0.66% of Direc) ! | Direct Ewald time 3.77 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.02% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 3.77 (85.51% of Nonbo) ! | Nonbond force 4.41 (66.23% of Force) ! | QMMM setup 0.04 ( 1.79% of QMMM ) ! | QMMM list build 0.02 ( 0.78% of QMMM ) ! | QMMM prep coords 0.01 ( 0.41% of QMMM ) ! | QMMM scf 2.18 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.18 (96.88% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.08% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.05% of QMMM ) ! | QMMM 2.25 (33.75% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 6.66 (98.44% of Runmd) ! | Shake time 0.02 ( 0.23% of Runmd) ! | Verlet update time 0.09 ( 1.31% of Runmd) ! | Other 0.00 ( 0.03% of Runmd) ! | Runmd Time 6.76 (97.62% of Total) ! | Other 0.14 ( 2.02% of Total) ! | Total time 6.93 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 14:12:56.178 on 04/17/2007 ! | Setup done at 14:12:56.342 on 04/17/2007 ! | Run done at 14:13:03.103 on 04/17/2007 | wallclock() was called 600 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center_md.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center_md.save 2007-04-17 14:14:27.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:47:48 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:49 [-O]verwriting output File Assignments: *************** *** 158,164 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 158,164 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 183,197 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 183,197 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 408,443 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.11% of Total) ! | Build the list 0.62 (98.76% of List ) ! | Other 0.01 ( 1.24% of List ) ! | List time 0.63 (13.53% of Nonbo) ! | Short_ene time 3.98 (98.96% of Direc) ! | Other 0.04 ( 1.04% of Direc) ! | Direct Ewald time 4.02 (99.90% of Ewald) ! | Force Adjust 0.00 ( 0.05% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 4.03 (86.47% of Nonbo) ! | Nonbond force 4.66 (13.94% of Force) ! | QMMM setup 0.06 ( 0.20% of QMMM ) ! | QMMM list build 0.01 ( 0.04% of QMMM ) ! | QMMM prep coords 0.01 ( 0.04% of QMMM ) ! | QMMM scf 28.64 (100.0% of QMMM ) ! | QMMM energy 28.64 (99.69% of QMMM ) ! | QMMM QM-MM force 0.01 ( 0.02% of QMMM ) ! | QMMM 28.73 (86.05% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 33.39 (99.16% of Runmd) ! | Shake time 0.02 ( 0.07% of Runmd) ! | Verlet update time 0.25 ( 0.74% of Runmd) ! | Other 0.01 ( 0.03% of Runmd) ! | Runmd Time 33.67 (99.33% of Total) ! | Other 0.19 ( 0.56% of Total) ! | Total time 33.90 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 10:47:48.348 on 03/13/2006 ! | Setup done at 10:47:48.575 on 03/13/2006 ! | Run done at 10:48:22.251 on 03/13/2006 | wallclock() was called 600 times --- 408,446 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.34% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.57 (99.31% of List ) ! | Other 0.00 ( 0.69% of List ) ! | List time 0.58 (13.57% of Nonbo) ! | Short_ene time 3.66 (99.35% of Direc) ! | Other 0.02 ( 0.65% of Direc) ! | Direct Ewald time 3.68 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.02% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 3.68 (86.43% of Nonbo) ! | Nonbond force 4.26 (65.80% of Force) ! | QMMM setup 0.04 ( 1.76% of QMMM ) ! | QMMM list build 0.01 ( 0.45% of QMMM ) ! | QMMM prep coords 0.01 ( 0.34% of QMMM ) ! | QMMM scf 2.16 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.16 (97.34% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.08% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 2.22 (34.19% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 6.48 (98.44% of Runmd) ! | Shake time 0.01 ( 0.22% of Runmd) ! | Verlet update time 0.09 ( 1.31% of Runmd) ! | Other 0.00 ( 0.02% of Runmd) ! | Runmd Time 6.58 (97.61% of Total) ! | Other 0.14 ( 2.04% of Total) ! | Total time 6.74 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 14:12:49.300 on 04/17/2007 ! | Setup done at 14:12:49.461 on 04/17/2007 ! | Run done at 14:12:56.044 on 04/17/2007 | wallclock() was called 600 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.img_center.save 2007-04-17 14:14:14.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:46:19 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:45 [-O]verwriting output File Assignments: *************** *** 148,154 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 148,154 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 173,187 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 173,187 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 336,370 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.03 ( 0.23% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.72 (99.27% of List ) ! | Other 0.01 ( 0.73% of List ) ! | List time 0.72 (28.27% of Nonbo) ! | Short_ene time 1.82 (98.94% of Direc) ! | Other 0.02 ( 1.06% of Direc) ! | Direct Ewald time 1.84 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.84 (71.73% of Nonbo) ! | Nonbond force 2.56 (19.22% of Force) ! | QMMM setup 0.06 ( 0.55% of QMMM ) ! | QMMM list build 0.01 ( 0.05% of QMMM ) ! | QMMM prep coords 0.01 ( 0.05% of QMMM ) ! | QMMM scf 10.69 (100.0% of QMMM ) ! | QMMM energy 10.69 (99.31% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.03% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 10.77 (80.75% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.03% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 13.34 (100.0% of Runmd) ! | Runmd Time 13.34 (97.41% of Total) ! | Other 0.32 ( 2.35% of Total) ! | Total time 13.69 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 10:46:19.393 on 03/13/2006 ! | Setup done at 10:46:19.624 on 03/13/2006 ! | Run done at 10:46:33.083 on 03/13/2006 | wallclock() was called 250 times --- 336,371 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.48% of Total) ! | Fast Water setup 0.00 ( 0.03% of Total) ! | Build the list 0.58 (99.50% of List ) ! | Other 0.00 ( 0.50% of List ) ! | List time 0.58 (25.85% of Nonbo) ! | Short_ene time 1.66 (99.35% of Direc) ! | Other 0.01 ( 0.65% of Direc) ! | Direct Ewald time 1.67 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.67 (74.15% of Nonbo) ! | Nonbond force 2.25 (71.86% of Force) ! | QMMM setup 0.04 ( 4.43% of QMMM ) ! | QMMM list build 0.00 ( 0.52% of QMMM ) ! | QMMM prep coords 0.00 ( 0.41% of QMMM ) ! | QMMM scf 0.83 (100.0% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM energy 0.83 (94.50% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.10% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.04% of QMMM ) ! | QMMM 0.88 (28.05% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.08% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 3.14 (100.0% of Runmd) ! | Runmd Time 3.14 (93.46% of Total) ! | Other 0.20 ( 6.03% of Total) ! | Total time 3.35 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 769 ! | Job began at 14:12:45.862 on 04/17/2007 ! | Setup done at 14:12:46.034 on 04/17/2007 ! | Run done at 14:12:49.217 on 04/17/2007 | wallclock() was called 250 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged_md_pme.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged_md_pme.save 2007-04-17 14:14:48.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:50:37 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:11 [-O]verwriting output File Assignments: *************** *** 159,165 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION --- 159,165 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 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 *************** *** 186,200 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 186,200 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 424,470 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.12% of Total) ! | Build the list 0.27 (87.85% of List ) ! | Other 0.04 (12.15% of List ) ! | List time 0.30 ( 9.29% of Nonbo) ! | Short_ene time 2.08 (98.05% of Direc) ! | Other 0.04 ( 1.95% of Direc) ! | Direct Ewald time 2.12 (71.62% of Ewald) ! | Adjust Ewald time 0.01 ( 0.45% of Ewald) ! | Self Ewald time 0.00 ( 0.01% of Ewald) ! | Fill Bspline coeffs 0.04 ( 5.37% of Recip) ! | Fill charge grid 0.18 (21.82% of Recip) ! | Scalar sum 0.08 (10.22% of Recip) ! | Grad sum 0.20 (24.66% of Recip) ! | FFT time 0.30 (37.08% of Recip) ! | Other 0.01 ( 0.84% of Recip) ! | Recip Ewald time 0.82 (27.79% of Ewald) ! | Force Adjust 0.00 ( 0.05% of Ewald) ! | Virial junk 0.00 ( 0.07% of Ewald) ! | Other 0.00 ( 0.01% of Ewald) ! | Ewald time 2.96 (90.71% of Nonbo) ! | Nonbond force 3.26 (10.52% of Force) ! | QMMM setup 0.06 ( 0.21% of QMMM ) ! | QMMM list build 0.01 ( 0.04% of QMMM ) ! | QMMM prep coords 0.01 ( 0.04% of QMMM ) ! | QMMM scf 27.63 (100.0% of QMMM ) ! | QMMM energy 27.63 (99.67% of QMMM ) ! | QMMM QM-MM force 0.01 ( 0.02% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 27.73 (89.47% of Force) ! | Other 0.00 ( 0.01% of Force) ! | Force time 30.99 (99.10% of Runmd) ! | Shake time 0.02 ( 0.07% of Runmd) ! | Verlet update time 0.25 ( 0.80% of Runmd) ! | Other 0.01 ( 0.02% of Runmd) ! | Runmd Time 31.27 (99.24% of Total) ! | Other 0.20 ( 0.64% of Total) ! | Total time 31.51 (100.0% of ALL ) | Highest rstack allocated: 627912 | Highest istack allocated: 12612 ! | Job began at 10:50:37.398 on 03/13/2006 ! | Setup done at 10:50:37.637 on 03/13/2006 ! | Run done at 10:51:08.906 on 03/13/2006 | wallclock() was called 765 times --- 424,470 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.49% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Build the list 0.26 (89.85% of List ) ! | Other 0.03 (10.15% of List ) ! | List time 0.29 (12.13% of Nonbo) ! | Short_ene time 1.64 (98.51% of Direc) ! | Other 0.02 ( 1.49% of Direc) ! | Direct Ewald time 1.66 (79.04% of Ewald) ! | Adjust Ewald time 0.01 ( 0.65% of Ewald) ! | Fill Bspline coeffs 0.02 ( 5.37% of Recip) ! | Fill charge grid 0.07 (16.44% of Recip) ! | Scalar sum 0.08 (17.90% of Recip) ! | Grad sum 0.09 (20.56% of Recip) ! | FFT time 0.17 (39.05% of Recip) ! | Other 0.00 ( 0.68% of Recip) ! | Recip Ewald time 0.42 (20.17% of Ewald) ! | Force Adjust 0.00 ( 0.03% of Ewald) ! | Virial junk 0.00 ( 0.10% of Ewald) ! | Ewald time 2.10 (87.87% of Nonbo) ! | Nonbond force 2.39 (51.75% of Force) ! | QMMM setup 0.04 ( 1.80% of QMMM ) ! | QMMM list build 0.01 ( 0.46% of QMMM ) ! | QMMM prep coords 0.01 ( 0.37% of QMMM ) ! | QMMM scf 2.17 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.17 (97.26% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.08% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 2.23 (48.23% of Force) ! | Other 0.00 ( 0.02% of Force) ! | Force time 4.62 (97.77% of Runmd) ! | Shake time 0.02 ( 0.32% of Runmd) ! | Verlet update time 0.09 ( 1.88% of Runmd) ! | Other 0.00 ( 0.04% of Runmd) ! | Runmd Time 4.73 (96.56% of Total) ! | Other 0.14 ( 2.93% of Total) ! | Total time 4.89 (100.0% of ALL ) | Highest rstack allocated: 627912 | Highest istack allocated: 12612 ! | Job began at 14:12:11.347 on 04/17/2007 ! | Setup done at 14:12:11.515 on 04/17/2007 ! | Run done at 14:12:16.240 on 04/17/2007 | wallclock() was called 765 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged_md.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged_md.save 2007-04-17 14:14:39.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:49:17 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:04 [-O]verwriting output File Assignments: *************** *** 158,164 **** QMMM: qm_charge = 1 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 = -2.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 158,164 ---- QMMM: qm_charge = 1 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 = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 183,197 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 183,197 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 408,444 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.11% of Total) ! | Build the list 0.63 (98.74% of List ) ! | Other 0.01 ( 1.26% of List ) ! | List time 0.64 (13.60% of Nonbo) ! | Short_ene time 3.99 (98.92% of Direc) ! | Other 0.04 ( 1.08% of Direc) ! | Direct Ewald time 4.03 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.04% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 4.04 (86.40% of Nonbo) ! | Nonbond force 4.67 (14.05% of Force) ! | QMMM setup 0.06 ( 0.20% of QMMM ) ! | QMMM list build 0.01 ( 0.04% of QMMM ) ! | QMMM prep coords 0.01 ( 0.04% of QMMM ) ! | QMMM scf 28.48 (100.0% of QMMM ) ! | QMMM energy 28.48 (99.69% of QMMM ) ! | QMMM QM-MM force 0.01 ( 0.02% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 28.57 (85.94% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 33.24 (99.17% of Runmd) ! | Shake time 0.02 ( 0.07% of Runmd) ! | Verlet update time 0.25 ( 0.74% of Runmd) ! | Other 0.01 ( 0.02% of Runmd) ! | Runmd Time 33.52 (99.21% of Total) ! | Other 0.23 ( 0.68% of Total) ! | Total time 33.79 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 10:49:17.665 on 03/13/2006 ! | Setup done at 10:49:17.933 on 03/13/2006 ! | Run done at 10:49:51.453 on 03/13/2006 | wallclock() was called 600 times --- 408,446 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.34% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.58 (99.33% of List ) ! | Other 0.00 ( 0.67% of List ) ! | List time 0.59 (13.66% of Nonbo) ! | Short_ene time 3.68 (99.34% of Direc) ! | Other 0.02 ( 0.66% of Direc) ! | Direct Ewald time 3.70 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.02% of Ewald) | Virial junk 0.00 ( 0.05% of Ewald) ! | Ewald time 3.71 (86.33% of Nonbo) ! | Nonbond force 4.29 (65.69% of Force) ! | QMMM setup 0.04 ( 1.76% of QMMM ) ! | QMMM list build 0.01 ( 0.44% of QMMM ) ! | QMMM prep coords 0.01 ( 0.35% of QMMM ) ! | QMMM scf 2.18 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 2.18 (97.34% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.08% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 2.24 (34.30% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 6.53 (98.46% of Runmd) ! | Shake time 0.01 ( 0.22% of Runmd) ! | Verlet update time 0.09 ( 1.29% of Runmd) ! | Other 0.00 ( 0.03% of Runmd) ! | Runmd Time 6.64 (97.40% of Total) ! | Other 0.15 ( 2.25% of Total) ! | Total time 6.81 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 14:12:04.395 on 04/17/2007 ! | Setup done at 14:12:04.572 on 04/17/2007 ! | Run done at 14:12:11.208 on 04/17/2007 | wallclock() was called 600 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged.save 2006-04-03 18:15:09.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_periodic/mdout.notimaged.save 2007-04-17 14:14:32.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:48:37 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:12:00 [-O]verwriting output File Assignments: *************** *** 148,154 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 148,154 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 173,187 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 173,187 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 336,370 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.03 ( 0.24% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.64 (99.17% of List ) ! | Other 0.01 ( 0.83% of List ) ! | List time 0.64 (25.90% of Nonbo) ! | Short_ene time 1.82 (98.91% of Direc) ! | Other 0.02 ( 1.09% of Direc) ! | Direct Ewald time 1.84 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.84 (74.09% of Nonbo) ! | Nonbond force 2.49 (18.67% of Force) ! | QMMM setup 0.06 ( 0.53% of QMMM ) ! | QMMM list build 0.01 ( 0.05% of QMMM ) ! | QMMM prep coords 0.01 ( 0.05% of QMMM ) ! | QMMM scf 10.77 (100.0% of QMMM ) ! | QMMM energy 10.77 (99.33% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.03% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.01% of QMMM ) ! | QMMM 10.84 (81.30% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.03% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 13.34 (100.0% of Runmd) ! | Runmd Time 13.34 (97.25% of Total) ! | Other 0.34 ( 2.51% of Total) ! | Total time 13.71 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 10:48:37.237 on 03/13/2006 ! | Setup done at 10:48:37.491 on 03/13/2006 ! | Run done at 10:48:50.950 on 03/13/2006 | wallclock() was called 250 times --- 336,371 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.51% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Build the list 0.59 (99.48% of List ) ! | Other 0.00 ( 0.52% of List ) ! | List time 0.59 (25.61% of Nonbo) ! | Short_ene time 1.71 (99.31% of Direc) ! | Other 0.01 ( 0.69% of Direc) ! | Direct Ewald time 1.73 (100.0% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) ! | Ewald time 1.73 (74.39% of Nonbo) ! | Nonbond force 2.32 (71.75% of Force) ! | QMMM setup 0.04 ( 4.40% of QMMM ) ! | QMMM list build 0.00 ( 0.51% of QMMM ) ! | QMMM prep coords 0.00 ( 0.43% of QMMM ) ! | QMMM scf 0.86 (100.0% of QMMM ) ! | Other 0.00 ( 0.02% of QMMM ) ! | QMMM energy 0.86 (94.52% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.10% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.04% of QMMM ) ! | QMMM 0.91 (28.16% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.08% of Force) | Other 0.00 ( 0.01% of Force) ! | Force time 3.24 (100.0% of Runmd) ! | Runmd Time 3.24 (93.12% of Total) ! | Other 0.22 ( 6.35% of Total) ! | Total time 3.47 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 767 ! | Job began at 14:12:00.756 on 04/17/2007 ! | Setup done at 14:12:00.947 on 04/17/2007 ! | Run done at 14:12:04.231 on 04/17/2007 | wallclock() was called 250 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut/MG_QM_water_MM_MD.out.save 2006-04-03 18:15:12.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut/MG_QM_water_MM_MD.out.save 2007-04-17 14:12:59.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:52:00 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:57 [-O]verwriting output File Assignments: *************** *** 147,153 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 147,153 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 172,186 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 172,186 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 400,434 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.04 ( 0.15% of Total) ! | Build the list 0.18 (98.58% of List ) ! | Other 0.00 ( 1.42% of List ) ! | List time 0.18 (12.66% of Nonbo) ! | Short_ene time 1.27 (99.67% of Direc) ! | Other 0.00 ( 0.33% of Direc) ! | Direct Ewald time 1.27 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.06% of Ewald) ! | Other 0.00 ( 0.01% of Ewald) ! | Ewald time 1.27 (87.33% of Nonbo) ! | Nonbond force 1.46 ( 5.84% of Force) ! | QMMM setup 0.06 ( 0.24% of QMMM ) ! | QMMM list build 0.01 ( 0.05% of QMMM ) ! | QMMM scf 23.36 (100.0% of QMMM ) ! | QMMM energy 23.36 (99.69% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.01% of QMMM ) ! | QMMM 23.44 (94.13% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.01% of Force) ! | Other 0.00 ( 0.01% of Force) ! | Force time 24.90 (97.97% of Runmd) ! | Verlet update time 0.51 ( 2.02% of Runmd) | Other 0.00 ( 0.01% of Runmd) ! | Runmd Time 25.41 (99.46% of Total) ! | Other 0.10 ( 0.39% of Total) ! | Total time 25.55 (100.0% of ALL ) | Highest rstack allocated: 3950 | Highest istack allocated: 790 ! | Job began at 10:52:00.940 on 03/13/2006 ! | Setup done at 10:52:01.077 on 03/13/2006 ! | Run done at 10:52:26.491 on 03/13/2006 | wallclock() was called 532 times --- 400,437 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.61% of Total) ! | Fast Water setup 0.00 ( 0.01% of Total) ! | Build the list 0.17 (99.44% of List ) ! | Other 0.00 ( 0.56% of List ) ! | List time 0.17 (12.70% of Nonbo) ! | Short_ene time 1.18 (99.85% of Direc) ! | Other 0.00 ( 0.15% of Direc) ! | Direct Ewald time 1.18 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.03% of Ewald) ! | Ewald time 1.18 (87.30% of Nonbo) ! | Nonbond force 1.35 (41.35% of Force) ! | QMMM setup 0.04 ( 2.10% of QMMM ) ! | QMMM list build 0.01 ( 0.55% of QMMM ) ! | QMMM prep coords 0.00 ( 0.02% of QMMM ) ! | QMMM scf 1.86 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 1.86 (97.26% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.04% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 1.91 (58.50% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.08% of Force) ! | Other 0.00 ( 0.07% of Force) ! | Force time 3.27 (93.78% of Runmd) ! | Verlet update time 0.22 ( 6.20% of Runmd) | Other 0.00 ( 0.01% of Runmd) ! | Runmd Time 3.48 (97.44% of Total) ! | Other 0.07 ( 1.94% of Total) ! | Total time 3.58 (100.0% of ALL ) | Highest rstack allocated: 3950 | Highest istack allocated: 790 ! | Job began at 14:11:57.050 on 04/17/2007 ! | Setup done at 14:11:57.142 on 04/17/2007 ! | Run done at 14:12:00.625 on 04/17/2007 | wallclock() was called 532 times *** test/qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut/MG_QM_water_MM.out.save 2006-04-03 18:15:12.000000000 -0700 --- test/qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut/MG_QM_water_MM.out.save 2007-04-17 14:12:54.000000000 -0700 *************** *** 3,9 **** Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 03/13/2006 at 10:51:38 [-O]verwriting output File Assignments: --- 3,9 ---- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 04/17/2007 at 14:11:54 [-O]verwriting output File Assignments: *************** *** 141,147 **** QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = -1.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- --- 141,147 ---- QMMM: qm_charge = 1 QMMM: QM atom RESP charge sum (inc MM link) = 1.000 QMMM: Adjusting each MM atom resp charge by = 0.000 ! QMMM: Sum of MM + QM region is now = 0.000 QMMM: ---------------------------------------------------------------------- --------------------------------------------------- *************** *** 166,180 **** Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9/serial/dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9/serial/dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9/serial/dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9/serial/dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9/serial/dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9/serial/dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9/serial/dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9/serial/dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9/serial/dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- --- 166,180 ---- Parameter files: TYP (AT) TYP (AT) SK integral FILE ! | 1 1 (c ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/cc.spl ! | 2 1 (c ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/ch.spl ! | 3 1 (c ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/cn.spl ! | 4 2 (h ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/hc.spl ! | 5 2 (h ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/hh.spl ! | 6 2 (h ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/hn.spl ! | 7 3 (n ) 1 (c ) /usr/local/amber9_release/amber9_new//dat/slko/nc.spl ! | 8 3 (n ) 2 (h ) /usr/local/amber9_release/amber9_new//dat/slko/nh.spl ! | 9 3 (n ) 3 (n ) /usr/local/amber9_release/amber9_new//dat/slko/nn.spl | QMMM: Estimated QM Dynamic Memory Usage (per thread) | QMMM: --------------------------------------------------- *************** *** 374,407 **** 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.10% of Total) ! | Build the list 0.14 (99.28% of List ) ! | Other 0.00 ( 0.72% of List ) ! | List time 0.14 (12.91% of Nonbo) ! | Short_ene time 0.92 (99.55% of Direc) ! | Other 0.00 ( 0.45% of Direc) ! | Direct Ewald time 0.92 (100.0% of Ewald) ! | Force Adjust 0.00 ( 0.01% of Ewald) | Other 0.00 ( 0.01% of Ewald) ! | Ewald time 0.92 (87.08% of Nonbo) ! | Nonbond force 1.06 ( 5.41% of Force) ! | QMMM setup 0.06 ( 0.31% of QMMM ) ! | QMMM list build 0.01 ( 0.05% of QMMM ) ! | QMMM prep coords 0.00 ( 0.01% of QMMM ) ! | QMMM scf 18.45 (100.0% of QMMM ) ! | QMMM energy 18.45 (99.61% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.02% of QMMM ) ! | QMMM 18.52 (94.56% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.02% of Force) ! | Other 0.00 ( 0.02% of Force) ! | Force time 19.59 (100.0% of Runmd) ! | Runmd Time 19.59 (98.97% of Total) ! | Other 0.18 ( 0.93% of Total) ! | Total time 19.79 (100.0% of ALL ) | Highest rstack allocated: 2260 | Highest istack allocated: 452 ! | Job began at 10:51:38.418 on 03/13/2006 ! | Setup done at 10:51:38.538 on 03/13/2006 ! | Run done at 10:51:58.212 on 03/13/2006 | wallclock() was called 490 times --- 374,409 ---- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.01 ( 0.42% of Total) ! | Fast Water setup 0.00 ( 0.02% of Total) ! | Build the list 0.12 (99.55% of List ) ! | Other 0.00 ( 0.45% of List ) ! | List time 0.12 (12.57% of Nonbo) ! | Short_ene time 0.83 (99.77% of Direc) ! | Other 0.00 ( 0.23% of Direc) ! | Direct Ewald time 0.83 (100.0% of Ewald) | Other 0.00 ( 0.01% of Ewald) ! | Ewald time 0.83 (87.43% of Nonbo) ! | Nonbond force 0.95 (38.09% of Force) ! | QMMM setup 0.04 ( 2.54% of QMMM ) ! | QMMM list build 0.01 ( 0.59% of QMMM ) ! | QMMM prep coords 0.00 ( 0.02% of QMMM ) ! | QMMM scf 1.50 (100.0% of QMMM ) ! | Other 0.00 ( 0.01% of QMMM ) ! | QMMM energy 1.50 (96.76% of QMMM ) ! | QMMM QM-MM force 0.00 ( 0.06% of QMMM ) ! | QMMM Collate Forces 0.00 ( 0.03% of QMMM ) ! | QMMM 1.55 (61.72% of Force) ! | Bond/Angle/Dihedral 0.00 ( 0.10% of Force) ! | Other 0.00 ( 0.09% of Force) ! | Force time 2.50 (100.0% of Runmd) ! | Runmd Time 2.50 (94.55% of Total) ! | Other 0.13 ( 5.01% of Total) ! | Total time 2.65 (100.0% of ALL ) | Highest rstack allocated: 2260 | Highest istack allocated: 452 ! | Job began at 14:11:54.273 on 04/17/2007 ! | Setup done at 14:11:54.391 on 04/17/2007 ! | Run done at 14:11:56.922 on 04/17/2007 | wallclock() was called 490 times ------------------------------------------------------------------------------ Temporary workarounds: none