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Martin Kurečka
Plumed AlphaFold
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8ff02bba
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Commit
8ff02bba
authored
10 years ago
by
Giovanni Bussi
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fixed char encoding
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cf38caae
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user-doc/tutorials/belfast-4.txt
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user-doc/tutorials/belfast-4.txt
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8ff02bba
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@@ -222,7 +222,7 @@ We here use a a model system alanine dipeptide with CHARM27 all atom force field
\subsection belfast-4-restrained-simulations Restrained simulations
The simplest way in which one
might in
fl
uence a CV is by forcing the system to stay close to a chosen
might in
fl
uence a CV is by forcing the system to stay close to a chosen
value during the simulation. This is achieved with a restraining potential
that PLUMED provides via the directive \ref RESTRAINT.
In the umbrella sampling method a bias potential is added so as
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@@ -283,7 +283,7 @@ the fifth the additional potential introduced by the restraint on \f$\psi\f$.
It may happen that one wants that a given CV just stays
within a given range of values. This is achieved in plumed through the
directives \ref UPPER_WALLS and \ref LOWER_WALLS that act on speci
fi
c collective variables and
directives \ref UPPER_WALLS and \ref LOWER_WALLS that act on speci
fi
c collective variables and
limit the exploration within given ranges.
\subsection belfast-4-reweighting Reweighting the results
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@@ -483,7 +483,7 @@ You can use the script that you used earlier to compute histogram.
The fact that when you add a force on the collective variable
PLUMED can force the atoms to do something depends on the fact that
the collective variables implemented in PLUMED has analytical
derivatives. By biasing the value of a single CV one turns to a
ff
ect
derivatives. By biasing the value of a single CV one turns to a
ff
ect
the time evolution of the system itself. Notice that some of the collective
variables could be implemented without derivatives (either because the
developers were lazy or because the CVs cannot be derived).
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