Molecular Dynamics

Molecular Dynamics Simulation

For electrons we have to solve the quantum Schroedinger Equation
For nuclei we only consider that they move classically
2

d x
dV

F ma m 2 mx
dt
dx

Force on nuclei can be obtained from potential derivative

x t t x t x t t

x t t x t x t t
xt 1 dV
m dx

x t

For example for harmonic oscillator

Initial Condition: You give starting geometry and

velocity then you calculate the force from your
potential energy surface. Using the force you
calculate the velocity and position change, then
continue on.

1
2
V x k x xeq
2
dV

k x xeq
dx

Types of Force Fields used in

Molecular Mechanics

V V0 cosa

12 6
V x 4
x
x

1
2
V x k x xeq
2
Wikipedia Molecular Mechanics

On the fly simulation

At every time step solve the electronic Schrodinger equation
Good Points
1. Accurate
2. Can describe reaction
3. Do not have to worry about fitting problems
Bad Points
1. Computational time is great so can only be used for
short time propagation
2. Can not perform detailed analysis

Gaussian 09 BOMD input

G09 BOMD output 1

G09 BOMD output 2

Method of Propagation1
Goal:

dx
f x, t ; xt0 x0 xt final in time step t
dt
Euler method (first order method take gradient)
xn 1 xn f xn , t n t

4th order Runge-Kutta propagation : add up

contribution along the way
1
xn 1 xn k1 2k 2 2k3 k 4 t
6
k1 f xn ,t n ;
k 2 f xn 0.5k1t , t n 0.5t

k3 f xn 0.5k 2 t , t n 0.5t ; k 4 f xn k3t , t n t

Method of Propagation 2
Predictor Corrector : repeated Euler
x1n 1 xn f xn , t n t

1
1
x xn f xn , t n f xn 1 , t n 1 t
2
1
3
xn 1 xn f xn , t n f xn21 , t n 1 t
2
...
2
n 1

1
m 1
x xn f xn , t n f xn 1 , t n 1 t
2
m
m 1
stop if xn 1 xn 1 threshold
m
n 1

Method of Propagation 3

Symplectic Integrator: special integrator for

classical mechanics made to satisfy Hamiltons
Equation dp
H
dq H

dt
q
dt p
Second order Symplectic assume H=T(p)+V(q)
V qn
t
pn 0.5 pn 0.5 p n t pn 0.5
q

T pn 0.5
qn 1 qn
t
p
V qn 1
t
pn 1 pn 0.5 0.5
q

Intermolecular Interaction: Super

Molecule Approximation

Super Molecule Approximation

To obtain the interaction between two waters perform
calculation of two waters

Two things to be careful

Size Consistency
Basis set super position erro

Size Consistancy

Consider H2H2 with CISD infinite far away

result for H2H2 is not equal to 2 H2!!

Two electron
excitation

H2A

H2A

H2B

H2A

H2B

Two electron excitation of

two H2 has four electron
excitation in H2H2

Two electron
excitation

H2A

H2B

H2A

H2A

H2B

Size Consistent Methods

MP2
CCSD
CCSD exp

T1 T2

D0

1
T1 D0 T2 D0 T1T1 D0 T2T2 D0 T1T2 D0
2
Pople et al. have defined an empirical estimation of the four electron
excitation contribution MRSDCI had defined +Q so for bond dissociation
and potential energy surface calculation people use MRSDCI+Q to
approximately take care of the size consistancy problem

Basis Set Super Position Error

When calculating the energy of a
supermolecule we use the basis set of
Molecule A and Molecule B together, when
we calculate the separated products we
calculate molecule A with basis of A, molecule
B with basis of B

VS

Counter Poise Correction

Boys Lanbardi method: use ghost atoms (no
charge just position to put basis)and put the
basis for the respective partner in the energy
calculation for molecule A and B

VS

BSSE big for small basis sets

Gaussian CP Input

G09 CP output 1

G09 CP output2

G09 CP output3

G09 CP output4

G09 CP Output 5

G09 CP output 6

Optimized Geometry CP

W/O CP

with CP

Excited Electronic States

Calculation

Method for Excited States

Use more than one slater determinant

CISD: Configuration Interaction Singles and Doubles

CCSD: Coupled Cluster Singles and Doubles
MCSCF: Multiconfigurational Self Consistent Field
MR-CISD: Multireference CISD

CAS MP2
MP2,3,4: Mollar Plesset perturbation theory

Equation of Motion CCSD

Time Dependent DFT