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The
Run functions described in this page can be called
only after the setup()
function. Run functions can be mixed with calls to
the Modify functions. Some functions return a
result code.
These
three functions take one argument each and no
keywords. The behavior of these functions may be
modified using the appropriate Modify
functions.
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Function
|
Summary
|
Return
Values
|
|
dynamics()
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integrate
the equations of motion to the specified
number of steps
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1
if criterion met, 0
otherwise
|
|
Keyword
|
Argument
|
Type
or Values
|
Interpretation
|
Initial
Value
|
|
.
|
#1
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Unsigned
|
number
of steps
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#0
|
|
Function
|
Summary
|
Return
Values
|
|
minimize()
|
minimize
the energy to the specified number of
steps or perhaps fewer
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1
if criterion met, 0
otherwise
|
|
Keyword
|
Argument
|
Type
or Values
|
Interpretation
|
Initial
Value
|
|
.
|
#1
|
Unsigned
|
number
of steps
|
#0
|
|
Function
|
Summary
|
Return
Values
|
|
montecarlo()
|
carry
out a Monte Carlo simulation to the
specified number of steps
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1
if criterion met, 0
otherwise
|
|
Keyword
|
Argument
|
Type
or Values
|
Interpretation
|
Initial
Value
|
|
.
|
#1
|
Unsigned
|
number
of steps
|
#0
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These
last remaining functions do not have arguments.
Note that you still have to write an empty pair of
parentheses after the function name. If you leave
out the parentheses, you may still have a legal
Python statement but it is probably not what you
intend.
Except
for the first and last, these functions do not
return any values.
|
Function
|
Summary
|
Return
Values
|
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archive()
|
archive
the current coordinates and/or velocities
now
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1
if OK, 0 otherwise
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updatelist()
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update
the non-bond lists now
|
#0
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backup()
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copy
current coordinates to
memory
|
#0
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restore()
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replace
coordinates with backup
copy
|
#0
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center()
|
move
the molecule so that the center of mass is
at the origin
|
#0
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energies()
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print
the energies on the standard
output
|
#0
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energy_rmsgrad()
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return
energy and RMS gradient in traditional
units
|
(
#f, #g )
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backup()
must be called before restore().
For each call to backup(),
restore()
may be called multiple times. Note that non-bond
list update and archive intervals can also be set
to occur at regular and independent intervals
within the Molecular Dynamics, Energy Minimization
and Monte Carlo methods.
Notes:
#0 : None
#1 : this argument does not have a keyword
#f : potential energy [kcal/mol]
#g : RMS gradient
[kcal/mol/Å]
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