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Martin Kurečka
Plumed AlphaFold
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406f97ef
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406f97ef
authored
4 years ago
by
Massimiliano Bonomi
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improving second ISDD tutorial
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user-doc/tutorials/a-master-ISDD-2.txt
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@@ -4,6 +4,9 @@
\section master-ISDD-2-aims Aims
The aim of this tutorial is to train users to perform metadynamics simulations with PLUMED.
This tutorial has been prepared by Max Bonomi (adapting a lot of material from other tutorials) for
the <a href="http://isddteach.sdv.univ-paris-diderot.fr/fr/accueil.html">Master In Silico Drug Design</a>, held
at Universite' de Paris on November 25th, 2020.
\section master-ISDD-2-objectives Learning Outcomes
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@@ -32,11 +35,11 @@ The archive can be unpacked using the following command:
tar xvzf master-ISDD-2.tar.gz
\endverbatim
This tutorial has been tested
on version 2.5.1
.
This tutorial has been tested
with PLUMED version 2.6.2 and GROMACS version 2019.6
.
\section master-ISDD-2-intro Introduction
W
e have seen that PLUMED can be used to compute collective variables. However, PLUMED
In the previous tutorial, w
e 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
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@@ -137,6 +140,7 @@ MOLINFO STRUCTURE=diala.pdb
# you might want to use MOLINFO shortcuts
phi: TORSION ATOMS=__FILL__
# Compute the backbone dihedral angle psi, defined by atoms N-CA-C-N
# here also you might want to use MOLINFO shortcuts
psi: TORSION ATOMS=__FILL__
# Activate well-tempered metadynamics in phi
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