Water Sept05
-
Upload
xavier-prat-resina -
Category
Business
-
view
248 -
download
3
Transcript of 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:
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
[ ] [ ]
'''
1'
2
1
''
2
1ˆ
0
2
0000
'0
0
nnnn
E
rr
EnnVnErr
nnHE
n
XC
iiXCXC
occ
iii
δδδδ
δ
ψψ
+
−+
+−+−
−=
∫∫
∫∫∫∑
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
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
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
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
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
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
−=
∞→
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
Switching waters: modeled systems
Collecting data between 1-4 ps has the same slope and less statistics
1:dhga2:hbond, gausw3: dhga, hbond, gausw
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
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+
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
3rd order: 5.5E-4 Å2/fsHbond: 7.2E-4 Å2/fs3rd+Hbond: 5.3E-4 Å2/fs
experimental9.3E-4 Å2/fs
5.8E-47.6E-45.8E-4
5.3E-46.7E-44.9E-4
effect of the QM size bigQM smallQM
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
H+
3rd order: 5.5E-4 Å2/fsHbond: 7.2E-4 Å2/fs3rd+Hbond: 5.3E-4 Å2/fs
experimental9.3E-4 Å2/fs
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
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
H+
identification of structural species: What molecule are we talking about?
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
H+
graph
Hydronium: H3O+Zundel: H5O2+Eigen: H9O3+
3rd order: 2.3E-4 Å2/fsHbond: 2.2E-4 Å2/fs3rd+Hbond: 2.0E-4 Å2/fs
experimental5E-4 Å2/fs
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
OH- : Herr doktor Haibo Yu
6
))0()(( 2rtr
dt
dDiff
−=
3rd order: 6.8E-4 Å2/fsHbond: 3.7E-4 Å2/fs3rd+Hbond: 2.8E-4 Å2/fs
experimental2.9E-4 Å2/fs
H2O
6
))0()(( 2rtr
dt
dDiff
−=
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
3rd order: 6.0E-4 Å2/fsHbond: 3.2E-4 Å2/fs3rd+Hbond: 2.1E-4 Å2/fs
experimental2.9E-4 Å2/fs
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
6
))0()(( 2rtr
dt
dDiff
−=
H2O 1st 5ps
Bibliography SCCdftb/MM SwitchWaters H3O+ OH- H2O
H2O: RDF gO-O