Chemistry Reference
In-Depth Information
(called pth_out_0000.log) gives the gradient of
at every
list
step. A value of
this gradient of 10 (kcal/mol)
2
or less typically produces a convergent trajec-
tory. Convergence can be analyzed by comparing intermediate results for the
paths, which are written after each cycle of optimization.
At the end of a run, the final trajectory is output (
file wcrd
) with path
format. MOIL contains several programs that can be used to analyze the tra-
jectory (computation of radius of gyration, native contacts, secondary struc-
ture content, etc). The Windows graphics interface of MOIL can be used to
visualize the trajectory. Also, the path format can be converted to a more con-
ventional format like
dcd
using the
ccrd
program of MOIL.
Dcd
files can be
open by many molecular visualization programs such as VMD.
121
The most common error message during a SDEL run is ''
Our momentum
0.'' This occurs any time the potential energy is larger than the total
energy during the optimization process. Changes of the annealing parameters
or the value of
<
is
g
often fix this problem.
Applications of the Stochastic Difference
Equation in Length
The SDEL algorithm has been used to study the folding dynamics of sev-
eral peptides and protein systems. In those applications the solvent environ-
ment was treated implicitly using the generalized Born model.
122,123
The
algorithm was first applied to study the folding of the B domain fragment of
the
Staphylococcal
protein A,
97
a 60-residue three-helical protein that has
been studied by many groups using different computational strategies.
107
An
experimental assessment of the transition state for this folding process high-
lights the difficulties of atomic simulations in capturing all the features
observed in the experiment.
124
The results from SDEL were similar to those
of high-temperature MD simulations, showing early formation of the most
stable helix. The experiment indicates that the other two helices are more
involved in the early folding, hinting that some energetic frustration may exist
during the folding of this protein.
125
SDEL was also used to study the coil-helix transition of an alanine-rich
peptide,
98
the conformational transition of sugar puckering in deoxyadeno-
sine,
126
polymerase P,
127
and the B-Z DNA transition.
128
The coil to helix
study
98
exemplified several properties of SDEL trajectories, like the filtering
of high-frequency modes and the preservation of thermodynamics properties
for slow degrees of freedom when the trajectory resolution is decreased.
An interesting application of SDEL involved the folding mechanism of
cytochrome c.
129
The folding kinetics of cytochrome c has been studied exten-
sively by a variety of experimental techniques.
130-134
The SDEL folding trajec-
tories agree with several experimental observations including: (1) the collapse of
the protein without formation of secondary structures followed by formation
of the terminal helices before the middle helix (see upper side of Figure 12),
