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Commit 406f97ef authored by Massimiliano Bonomi's avatar Massimiliano Bonomi
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improving second ISDD tutorial

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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
......@@ -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
We have seen that PLUMED can be used to compute collective variables. However, PLUMED
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
......@@ -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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