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Martin Kurečka
Plumed AlphaFold
Commits
094255ce
There was an error fetching the commit references. Please try again later.
Commit
094255ce
authored
11 years ago
by
Carlo Camilloni
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Reference added for MetaD acceleration factor
parent
0dd7799e
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src/bias/MetaD.cpp
+4
-4
4 additions, 4 deletions
src/bias/MetaD.cpp
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4 additions
and
4 deletions
src/bias/MetaD.cpp
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4
−
4
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094255ce
...
...
@@ -186,10 +186,10 @@ one update and the other.
\par
The kinetics of the transitions between basins can also be analysed on the fly as
in \cite
pratyush13prl
. The flag ACCELERATION turn on accumulation of the acceleration
in \cite
PRL230602
. The flag ACCELERATION turn on accumulation of the acceleration
factor that can then be used to determine the rate. This method can be used together
with \ref COMMITTOR analysis to stop the simulation when the system get to the target basin.
It must be used together with
w
ell-
t
empered
m
etadynamics.
It must be used together with
W
ell-
T
empered
M
etadynamics.
*/
//+ENDPLUMEDOC
...
...
@@ -483,7 +483,7 @@ isFirstStep(true)
addComponent
(
"bias"
);
componentIsNotPeriodic
(
"bias"
);
if
(
acceleration
)
{
if
(
!
welltemp_
)
error
(
"The calculation of the acceleration works only if Well
t
empered
m
etadynamics is on"
);
if
(
!
welltemp_
)
error
(
"The calculation of the acceleration works only if Well
-T
empered
M
etadynamics is on"
);
log
.
printf
(
" calculation on the fly of the acceleration factor"
);
addComponent
(
"acc"
);
componentIsNotPeriodic
(
"acc"
);
}
...
...
@@ -570,7 +570,7 @@ isFirstStep(true)
if
(
doInt_
)
log
<<
plumed
.
cite
(
"Baftizadeh, Cossio, Pietrucci, and Laio, Curr. Phys. Chem. 2, 79 (2012)"
);
if
(
acceleration
)
log
<<
plumed
.
cite
(
"Pratyush and Parrinello, Phys. Rev. Lett.
...
(2013)"
);
"Pratyush and Parrinello, Phys. Rev. Lett.
111, 230602
(2013)"
);
log
<<
"
\n
"
;
}
...
...
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