Water Sept05

Watera test for

SCCdftb/MM

Xavier Prat-ResinaFriday September 30, 2005 AD

Summary

1.Bibliography: molecular models of water

2.SCCdftb/MM:

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

Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O

SCCdftb/MM:


[ ] [ ]

'''

1'

2

1

''

2

1ˆ

0

2

0000

'0

0

nnnn

E

rr

EnnVnErr

nnHE

n

XC

iiXCXC

occ

iii

δδδδ

δ

ψψ

+

−+

+−+−

−=

∫∫

∫∫∫∑



Since solvent waters during a MD move in and move out of the QM/MM partitionwe will select dynamically the QM zone• Exchange MM water moving in by a QM water moving out• The composition of QM is always the same

Switching waters in the QM/MM selection

The waters that belong to the QM are reselected dynamically accordingto some criteria

•Around a point (fixed xyz or moving atom)

•Around two atoms

•Around the cylinder between two atoms

•Around the Center of excess charge (CEC)

•Around the closest proton or oxygen to the CEC


QM

QM

QM

QM

Switching waters: criteria to select the QM waters

∑∑∑∑ −⋅−−===

)()( ,11

ji

ij

jO

jH

iOz

HzHOsw

Oz

N

j

ON

i

Hzz rrdfrwrξ

(see vmd)

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*) endsccdftb 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

Solvated protonSolvated 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 atom90-150 atoms

SCCdftb: hbond (+gaussw);hbond+3rd order Hubbard3rd order Hubbard

Compute coefficient of diffusion and RDF

6

))0()((lim

2rtr

dt

dDiff

t

−=

∞→


Switching waters: modeled systems

Collecting data between 1-4 ps has the same slope and less statistics

1:dhga2:hbond, gausw3: dhga, hbond, gausw


6

))0()(( 2rtr

dt

dDiff

−=

3rd order: 5.5E-4 Å2/fsHbond: 7.2E-4 Å2/fs3rd+Hbond: 5.3E-4 Å2/fs

experimental9.3E-4 Å2/fs

H+




5.8E-47.6E-45.8E-4

5.3E-46.7E-44.9E-4

effect of the QM size bigQM smallQM


H+



6.0E-47.4E-45.7E-4

5.1E-46.1E-45.1E-4

effect of the edge of sphere 1st 2.5ps 2nd 2.5ps


H+

identification of structural species: What molecule are we talking about?


H+

graph

Hydronium: H3O+Zundel: H5O2+Eigen: H9O3+


experimental5E-4 Å2/fs


OH- : Herr doktor Haibo Yu

6

))0()(( 2rtr

dt

dDiff

−=



H2O

6

))0()(( 2rtr

dt

dDiff

−=





6

))0()(( 2rtr

dt

dDiff

−=

H2O 1st 5ps


H2O: RDF gO-O

Business

Water Sept05