Talk:Mod:Hunt Research Group/QMMM OPT Aqeuous Cu(II)
This ChemShell code runs a QM/MM geometry optimisation on our copper(II)-water system:
newopt function = copt : { coords=cu_18water.pun
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp }
mm_theory=dl_poly : mm_defs=ff.dat
}
result=cu_18water_qmmm_opt.pun
}
The newopt command invokes a general purpose optimiser code. The target function copt carries out the optimisation in Cartesian co-ordinates.
The initial co-ordinates are taken from here while the force field parameters were defined here.
To run the optimisation, login to cx1 and submit the code via the PBS queue system (details here).
If the optimisation is successful, you should see something like this at the end of the .out file:
-------------------------------------------------------------------------------- ******************************************************************************** Optimisation finished successfully ******************************************************************************** Results have been written to cu_18water_qmmm_opt.pun newopt/copt/===================================== Tstep: 0.0 Ttot:42371.2 == newopt/copt/hybrid.kill/========================= Tstep: 0.0 Ttot:42371.2 == ...hybrid.kill/dl_poly.kill/===================== Tstep: 0.0 Ttot:42371.2 == ******************************* DL_POLY finished ******************************* MM termination code: 0 Energy and gradient evaluations: QM energies 203 QM gradients 203 MM energies 203 MM gradients 203 no: end of optimisation ChemShell exiting code 0
The optimised structure is outputted into cu_18water_qmmm_opt.pun, which should look something like this:
block = fragment records = 0 block = title records = 1 molecule 1 block = coordinates records = 55 cu -3.76257780766541e+00 6.39581622755847e+00 4.18666084467700e+00 o -8.61211193402496e-02 7.64015048162733e-01 9.28566236359741e-01 h 1.21543269728197e+00 1.88270779646951e+00 1.31175606629519e-01 h 6.37781706300753e-01 -7.82734221778962e-02 2.38728556418122e+00 o -4.51642283433391e+00 8.77759819691374e+00 1.46678151077030e+00 h -3.49172990884007e+00 1.03072164818830e+01 1.11089581484648e+00 h -5.54866802060477e+00 8.25158794461243e+00 -1.97852968619387e-02 o -4.95471761998812e+00 8.71052570690642e+00 6.83662498793940e+00 h -4.05605484296627e+00 1.01570572540756e+01 7.49895970199808e+00 h -6.87371317404838e+00 8.63461596505159e+00 6.95816954313609e+00 o -9.51480700603425e+00 7.65268168973318e+00 6.49527652838249e+00 h -1.08191880350448e+01 8.52142478395586e+00 5.45922246856226e+00 h -1.02602478290014e+01 6.29462819566987e+00 7.55178619381274e+00 o 1.21783543029695e-02 8.18965965674802e+00 4.64643593288696e+00 h 1.70179143020656e+00 7.88361340447555e+00 3.95575265334706e+00 h 1.53560458819001e-02 9.55384358956816e+00 5.90422029240048e+00 o -4.02073293122077e+00 3.61793980085322e+00 1.74997219960407e+00 h -2.59371465606442e+00 2.44468654734398e+00 1.36433254970553e+00 h -5.67098509457942e+00 3.09821229178831e+00 1.07603574755595e+00 o -3.38985817557272e+00 3.79310802899656e+00 6.74770649250538e+00 h -3.25082227534437e+00 4.17399732561277e+00 8.58047932923543e+00 h -3.61597049183051e+00 1.96919514808289e+00 6.37114616477612e+00 o 4.88512549227045e+00 7.32303960143179e+00 3.03802690857829e+00 h 5.90371157876586e+00 6.25868175713396e+00 4.23890965743296e+00 h 5.97736349003507e+00 8.77594531470776e+00 2.48511559337944e+00 o -4.29916411874004e+00 -2.37226641024922e+00 8.55602074665862e-01 h -4.48197927494656e+00 -4.02399646204200e+00 -6.12604734180689e-02 h -2.77416381761238e+00 -1.45943015368469e+00 1.60090770859538e-01 o -1.15152916911611e+01 3.91507445983514e+00 9.09487558613262e+00 h -1.31397292921642e+01 4.04276654045411e+00 1.00694432162367e+01 h -1.08607626672630e+01 2.15038777612147e+00 9.32363260523809e+00 o -7.26161532617709e-01 1.18925561409003e+01 8.16570819162541e+00 h -3.38210015169806e-02 1.17120023508492e+01 9.92714273176291e+00 h -6.83632570128503e-01 1.37379782847602e+01 7.71682993448162e+00 o -2.02526336260395e+00 1.27938834288615e+01 5.91933212826634e-02 h -2.59260481593547e+00 1.45962476869073e+01 2.42272907816360e-01 h -6.60720242454038e-01 1.27504221632937e+01 -1.26012417899430e+00 o -3.94420311392931e+00 -9.99442342009302e-01 5.75664862690226e+00 h -4.25433895488514e+00 -1.52750992694953e+00 3.94311845980275e+00 h -4.00360780860933e+00 -2.57522517852673e+00 6.81366036938644e+00 o -1.30415098084718e+01 9.80484470829646e+00 3.78198257557867e+00 h -1.48929394074433e+01 9.81272313216625e+00 4.20334863832536e+00 h -1.27734330674330e+01 1.10379592139561e+01 2.36612507894359e+00 o 3.18343925559676e+00 3.99162245471456e+00 -7.01690759967063e-01 h 4.03998156283156e+00 4.31487863453482e+00 -2.36245736355065e+00 h 3.80617991301159e+00 5.30361078391041e+00 5.32356523409876e-01 o -7.34841503128147e+00 7.18270192875724e+00 -2.19006910801384e+00 h -8.06775536858874e+00 5.50688446733079e+00 -1.63361378230881e+00 h -7.98466645635603e+00 7.54260798655164e+00 -3.94099354583780e+00 o -8.74477062425801e+00 2.67357572335193e+00 2.06916587181714e-01 h -9.21569433472465e+00 1.05523926189405e+00 -6.69813132357446e-01 h -1.01226940595264e+01 3.05868782112006e+00 1.45407977156667e+00 o -3.09052434169466e+00 4.63395423526394e+00 1.16058757972695e+01 h -4.36175688579645e+00 5.67645850057569e+00 1.25528664304173e+01 h -1.86140317121958e+00 3.92461378513185e+00 1.28658799243406e+01 block = connectivity records = 38 1 5 1 17 2 3 2 4 5 6 5 7 8 9 8 10 11 12 11 13 14 15 14 16 17 18 17 19 20 21 20 22 23 24 23 25 26 27 26 28 29 30 29 31 32 33 32 34 35 36 35 37 38 39 38 40 41 42 41 43 44 45 44 46 47 48 47 49 50 51 50 52 53 54 53 55