Chemistry Reference
In-Depth Information
ð
X
Þ
p
, suggesting
that each conformation in the initial trajectory must have a potential energy
smaller than the total energy of the system. This, in turn, prevents the use of sim-
ple methods such as linear interpolation to compute the initial trajectory of the
two boundary structures; methods such as linear interpolation usually generate
intermediate structures with large potential energy due to steric repulsions.
In practice, this initial guess problem is solved by computing an approx-
imate MEP connecting the two boundary states. That path is then used as the
initial guess for SDEL. MOIL contains a program called
chmin
that computes
the MEP using a simple self-penalty walk algorithm.
77
Chmin
treats the path
as a polymer chain, where each monomer is a copy of the molecular system at
different times. The potential energy of the chain is the sum of the potential
energies of each monomer, with the addition of a harmonic attraction term
between nearest monomers, and an exponential repulsion term between
next nearest monomers.
The potential energy for the structures
V
2
step of the method. The SDEL action depends on
ð
E
V
in the MEP should be ana-
lyzed before using this trajectory as initial guess for SDEL. Not only must the
potential energy of every slice through the chain be lower than the total energy
of the system, but the potential energy should also vary smoothly along the
trajectory; steep peaks or decays of
V
ð
Y
i
Þ
ð
Y
i
Þ
can cause a numerical instability
during the optimization of the action.
The input file for SDEL, called path.inp in MOIL (Table 1), contains the
names for the file
with the initial guess trajectory (i.e., a binary file with
extension
pth
), and the molecule's connectivity file used to extract the poten-
tial parameters for the force field. The connectivity file (with extension
wcon
)
is generated by the program
conn
in MOIL.
The SDEL target function for optimization in MOIL is
ð
rcrd
Þ
2
þ
X
q
X
N
S
2
¼
0
g
ð
l
i
;
i
þ1
h
l
iÞ
½
37
q
Y
i
i
¼
Table 1
Example of Input File (path.inp) for SDEL
file conn name
¼
(val.wcon) unit
¼
10 read
file rcrd name
¼
(valmin200.pth) bina unit
¼
14 read
file wcrd name
¼
(valpath.PTH) bina unit
¼
12 wovr
#ste
¼
5000 list
¼
500
gama
¼
2000.0 grid
¼
200 pdqe
¼
42.2 gbsa
rmax
¼
9999. epsi
¼
1. v14f
¼
8. el14
¼
2. cpth
proc
¼
10
tmpr
¼
30000.0
dtop
¼
1.0d
4
anne
action
