Chemistry Reference
In-Depth Information
H
H
θ
O
(fixed)
θ
H
O
(fixed)
H
Figure 1
Planar water dimer model system. The dipole angle (measured from the
horizontal) is labeled as
y
.
The system is represented graphically in Figure 1. In the figure we indi-
cate the central dipole vector for one molecule. When analyzing the simulation
results, we will monitor the change of the angle
indicated in the figure.
The model uses natural units: angstroms, kilocalories per mole, and atomic
mass units (AKMA). In this system of units, lengths and masses have obvi-
ous values (e.g., a hydrogen atom has approximately unit mass), but the
resulting time unit is nonstandard: 4
y
10
14
s. For this reason a
time conversion is required so that simulation can be presented in time units
of femtoseconds (fs).
To begin, we must state explicitly the potential energy function. In this
example we use the CHARMM potential model:
13
:
888821
2
q
ð
k
ij
2
2
2
2
V
bond
ij
¼
x
i
x
j
Þ
þð
y
i
y
j
Þ
þð
y
i
y
j
Þ
L
ij
½
21
and
q
i
q
j
ð
V
elec
ij
¼
q
½
22
2
2
2
x
i
x
j
Þ
þð
y
i
y
j
Þ
þð
y
i
y
j
Þ
where the spring constants and equilibrium lengths for H-H and O-H bonds
are given by
k
HH
¼
450
:
0
k
OH
¼
450
:
0
L
OH
¼
0
:
9573
L
HH
¼
1
:
5139
and the electrostatic constants for hydrogen and oxygen are
q
H
¼
0
:
417
q
O
¼
0
:
834
