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Martin Kurečka
Plumed AlphaFold
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4 years ago
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Massimiliano Bonomi
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better intro to tutorial
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user-doc/tutorials/a-master-ISDD-2.txt
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@@ -44,12 +44,11 @@ tar xvzf master-ISDD-2.tar.gz
\section master-ISDD-2-intro Introduction
In the previous tutorial, we have seen that PLUMED can be used to compute collective variables. However, PLUMED
is most often use to add forces on the collective variables. To this aim,
we have implemented a variety of possible biases acting on collective variables.
The complete documentation for
all the biasing methods available in PLUMED can be found at the \ref Bias page.
In the following we will see how to build an adaptive bias potential with metadynamics.
In the previous tutorial, we have seen that PLUMED can be used to compute collective variables on a pre-calculated
trajectory. However, PLUMED is most often use to add forces on the collective variables during a MD simulation, for example,
in order to accelerate sampling. To this aim, we have implemented a variety of possible biases acting on collective variables.
The complete documentation for all the biasing methods available in PLUMED can be found at the \ref Bias page.
In the following we will learn how to use PLUMED to perform and analyze a metadynamics simulation.
Here you can find a brief recap of the metadynamics theory.
\hidden{Summary of theory}
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