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The
Modify functions described in this page can be
called only after the setup()
function. Modify functions can be mixed with calls
to the Run functions.
Specifying
a keyword value will store that value in
association with the keyword and for the associated
Run function. For example,
editminimizers()
modifies settings for the
minimize()
function; the settings are changed but have no
effect until minimize()
is called. The settings remain unchanged until
changed again by a call to the Modify
function.
|
Function
|
Summary
|
Return
Values
|
|
editmontecarlo()
|
Modify
the Monte Carlo methods
|
#0
|
|
Keyword
|
Argument
|
Type
or Values
|
Interpretation
|
Initial
Value
|
|
update_list
|
#2
|
Unsigned
|
nonbond
list update interval
|
25
|
|
report
|
#2
|
Unsigned
|
report
(printing) interval
|
1
|
|
adjust_step
|
#2
|
Unsigned
|
maximum
step size adjustment
interval
|
1
|
|
archive
|
#2
|
Unsigned
|
archive
interval
|
0
|
|
method
|
#2
|
"metropolis",
"rigid"
|
Monte
Carlo method
|
"metropolis"
|
|
dispose
|
#2
|
"yes",
"no"
|
deallocate
Monte Carlo data structure mapping on
completion?
|
"yes"
|
|
criterion
|
#2
|
Float
|
success
if acceptance ratio within this fraction
of target
|
0.1
|
|
acceptance_ratio
|
#2
|
Float
|
target
fraction of moves that are
accepted
|
0.5
|
|
step_size
|
#2
|
Float
|
initial
maximum step size
|
0.1
|
|
up_step
|
#2
|
Float
|
scale
up step size if exceeding accceptance
ratio
|
1.05
|
|
down_step
|
#2
|
Float
|
scale
down step size if not meeting acceptance
ratio
|
0.95
|
|
min_step
|
#2
|
Float
|
do
not adjust the maximum step size below
this value
[Å]
|
0.01
|
|
rigidstart
|
#2
|
Integer
|
first
atom number of this rigid
unit
|
-1
|
|
rigidend
|
#2
|
Integer
|
last
atom number of this rigid
unit
|
-1
|
|
rigidfrac
|
#2
|
0.0
to 1.0
|
fraction
of moves for this rigid unit that would be
rotation rather than
translation
|
0.0
|
|
minangle
|
#2
|
Float
|
do
not adjust the maximum rotation angle per
step below this value
[°]
|
0.01
|
|
maxdist
|
#2
|
Float
|
maximum
allowable displacement from the original
position (applies to Rigid only)
[Å]
|
1.0
|
|
stepangle
|
#2
|
Float
|
initial
maximum angle of rotation per step
[°]
|
0.1
|
There
are two Monte Carlo methods. The Metropolis method
moves each atom independently. The Rigid method
(which is still a Metropolis method) moves and
rotates rigid units independently. The Monte Carlo
methods are quite different from the other
Molecular Mechanics methods and access the force
field differently from the other methods.
Accordingly, the force field data structures are
remapped for efficient access by the Monte Carlo
methods. The remapping consumes memory but it is
returned to the operating system at the end of the
Monte Carlo procedure. You can set
dispose
to "no" in which case the extra data structures are
retained at the end of the Monte Carlo run. In
subsequent calls, there is no need for data
structure remapping. The remapping computation or
the extra memory are not significant in modern
computers. For the Rigid method, each rigid unit is
defined by calling editmontecarlo()
with the rigidstart,
rigidend
and rigidfrac
keywords. The rigid units must not overlap,
rigidstart
is less or equal to rigidend,
and the atom numbers in each subsequent rigid unit
must be larger than those of the previous.
Specifications that do not meet these rules are
quietly ignored (Note the initial values). If
rigidstart
= rigidend
= 0, the rigid units are destroyed. You can then
define a different sequence of rigid
units.
Notes:
#0 : none or no value
#1 : this argument must always be specified
#2 : this argument is optional
#3 : not applicable
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