3. Modelling water Classical approximations (no explicit treatment of electrons) SP5, EVB (Stillinger, Warshel, Voth, Tuckerman) Full QM systems Lagrangian: CPMD (Parrinello, Pratt), ADMP(Voth,Iyengar) Linear Scaling: Siesta, Divide and Conquer QM/MM Ab initio/MM: Rode neutral water, acid, basic, autoionization, phase transition SCCdftb/MM: Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
9. Build a list of distances of QM and MM waters with respect to the point. If r(O-MM) + swpr < r(O-QM) the switch is performed on the XYZ arrays (not for minimization!!) Every swfq steps the lists are checked and updated rxncor: define pcec sele (qm .and. type O*) end sele (qm .and. type H*) end sccdftb remove chrg 1 sele qm end TEMP 0.00 scft 0.00000001 – swit sele (qm .and. type O*) end sele ((.not. qm) .and. type O* ) end swop 6 swfq 1 swpr 1.5 Update nonbonded lists In our systems we ususally switch a water every 50 steps MD QM/MM Switching waters: implementation in charmm Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
10.
11. Solvated proton Solvated OH - Neutral water A 22 angstr. sphere of TIP3 waters with GSBP 300 K with Langevin 20-22 angst., SHAKE for MM, 1fs timestep QM: 6 angstr. around the target atom 90-150 atoms SCCdftb: hbond (+gaussw); hbond+3 rd order Hubbard 3 rd order Hubbard Compute coefficient of diffusion and RDF Switching waters: modeled systems Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
12. Collecting data between 1-4 ps has the same slope and less statistics 1:dhga 2:hbond, gausw 3: dhga, hbond, gausw Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
13. 3 rd order: 5.5E-4 Å 2 /fs Hbond: 7.2E-4 Å 2 /fs 3 rd +Hbond: 5.3E-4 Å 2 /fs experimental 9.3E-4 Å 2 /fs H + Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
14. 3 rd order: 5.5E-4 Å 2 /fs Hbond: 7.2E-4 Å 2 /fs 3 rd +Hbond: 5.3E-4 Å 2 /fs experimental 9.3E-4 Å 2 /fs 5.8E-4 7.6E-4 5.8E-4 5.3E-4 6.7E-4 4.9E-4 effect of the QM size bigQM smallQM H + Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
15. 3 rd order: 5.5E-4 Å 2 /fs Hbond: 7.2E-4 Å 2 /fs 3 rd +Hbond: 5.3E-4 Å 2 /fs experimental 9.3E-4 Å 2 /fs 6.0E-4 7.4E-4 5.7E-4 5.1E-4 6.1E-4 5.1E-4 effect of the edge of sphere 1 st 2.5ps 2 nd 2.5ps H + Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
16. identification of structural species: What molecule are we talking about? H + graph Hydronium: H3O+ Zundel: H5O2+ Eigen: H9O3+ Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
17. 3 rd order: 2.3E-4 Å 2 /fs Hbond: 2.2E-4 Å 2 /fs 3 rd +Hbond: 2.0E-4 Å 2 /fs experimental 5E-4 Å 2 /fs OH - : Herr doktor Haibo Yu Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
18. 3 rd order: 6.8E-4 Å 2 /fs Hbond: 3.7E-4 Å 2 /fs 3 rd +Hbond: 2.8E-4 Å 2 /fs experimental 2.9E-4 Å 2 /fs H 2 O Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
19. 3 rd order: 6.0E-4 Å 2 /fs Hbond: 3.2E-4 Å 2 /fs 3 rd +Hbond: 2.1E-4 Å 2 /fs experimental 2.9E-4 Å 2 /fs H 2 O 1 st 5ps Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
20. H 2 O: RDF gO-O Bibliography SCCdftb/MM SwitchWaters H 3 O + OH - H 2 O
