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Martin Kurečka
Plumed AlphaFold
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9f36e283
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Commit
9f36e283
authored
7 years ago
by
Massimiliano Bonomi
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add biasfactor
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6fc9d976
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user-doc/tutorials/a-trieste-4.txt
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user-doc/tutorials/a-trieste-4.txt
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9f36e283
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@@ -133,9 +133,10 @@ psi: TORSION ATOMS=__FILL__
# Activate well-tempered metadynamics in phi
metad: __FILL__ ARG=__FILL__ ...
# Deposit a Gaussian every 500 time steps, with initial height equal
# to 1.2 kJoule/mol, biasfactor equal to 10.0
PACE=500 HEIGHT=1.2 BIASFACTOR=10.0
# Deposit a Gaussian every 500 time steps, with initial height equal to 1.2 kJoule/mol
PACE=500 HEIGHT=1.2
# the bias factor should be wisely chosen
BIASFACTOR=__FILL__
# Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
SIGMA=__FILL__
# Gaussians will be written to file and also stored on grid
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@@ -335,7 +336,7 @@ psi: TORSION ATOMS=__FILL__
# Activate well-tempered metadynamics in phi
metad: __FILL__ ARG=__FILL__ ...
# Set the deposition stride to a large number
PACE=10000000 HEIGHT=1.2 BIASFACTOR=
10.0
PACE=10000000 HEIGHT=1.2 BIASFACTOR=
__FILL__
# Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
SIGMA=__FILL__
# Gaussians will be read from file and stored on grid
...
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