From 5f5b0e77d8685098dd5fac6c46d4d8373de5ef38 Mon Sep 17 00:00:00 2001
From: Massimiliano Bonomi <massimiliano.bonomi@gmail.com>
Date: Sat, 23 Oct 2021 06:46:19 +0200
Subject: [PATCH] update to 2021
---
user-doc/tutorials/aa-master-ISDD-1.txt | 129 +++++++++++-------------
user-doc/tutorials/aa-master-ISDD-2.txt | 6 +-
2 files changed, 61 insertions(+), 74 deletions(-)
diff --git a/user-doc/tutorials/aa-master-ISDD-1.txt b/user-doc/tutorials/aa-master-ISDD-1.txt
index 9420658e3..654c61e11 100644
--- a/user-doc/tutorials/aa-master-ISDD-1.txt
+++ b/user-doc/tutorials/aa-master-ISDD-1.txt
@@ -1,5 +1,5 @@
/**
-\page master-ISDD-1 Master ISDD tutorial 2020: Brief introduction to PLUMED
+\page master-ISDD-1 Master ISDD tutorial 2021: Brief introduction to PLUMED
\section master-ISDD-1-aims Aims
@@ -7,9 +7,9 @@ The aim of this tutorial is to introduce users to the PLUMED syntax. We will go
and print simple collective variables on a pre-calculated trajectory. 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.
+at Universite' de Paris on October 26th, 2021.
-\section master-ISDD-1-lo Learning Outcomes
+\section master-ISDD-1-lo Aims
Once this tutorial is completed, users will be able to:
@@ -18,105 +18,101 @@ Once this tutorial is completed, users will be able to:
- Use \ref MOLINFO shortcuts.
- Define and use virtual atoms, such as \ref CENTER.
-\section master-ISDD-1-install Software overview
+\section master-ISDD-1-install Software
In this and in the next tutorial, we will use two pieces of software: <a href="https://www.plumed.org">PLUMED</a> version 2.6.2 and
-<a href="http://www.gromacs.org">GROMACS</a> version 2019.6. Both codes have already been installed on your machines and are ready to use. If you are attending the tutorial on Zoom, please have a look below at the section "Install GROMACS+PLUMED on your own machine with Conda".
+<a href="http://www.gromacs.org">GROMACS</a> version 2019.6. First, we need to install the software on your machine using Conda.
-\subsection master-ISDD-1-plumed PLUMED
-
-PLUMED is a library that can be incorporated into many MD codes by adding a relatively simple and well documented interface.
-Once it is incorporated you can use PLUMED to perform a variety of different analyses on-the-fly and to bias
-the sampling in MD simulations. Additionally, PLUMED can be used as a standalone code for analyzing trajectories.
-If you are using the code in this way you can run the PLUMED executable by issuing the command:
+\subsection master-ISDD-1-install Installation
+
+First, check if Conda is installed on your machine by typing:
\verbatim
-plumed <instructions>
+conda
\endverbatim
-Let's start by getting a feel for the range of calculations that PLUMED can do. Issue the following command now:
+In case the command is not found, please follow the instructions below to install Conda in the
+directory `/path/to/conda`. You can choose it in your home so that you will have write permission to it.
\verbatim
-plumed --help
+# on Linux:
+wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+# on MacOS:
+# wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
+bash ./miniconda.sh -b -f -p /path/to/conda
+# export PATH to find the Conda executable
+export PATH="/path/to/conda/bin:$PATH"
+# initialize bash shell
+conda init bash
\endverbatim
-The output of this command is a list of tasks that PLUMED can perform. Among these, there are commands that allow you
-to patch an MD code, postprocess metadynamics simulations, and build the manual. In this
-tutorial we will mostly use PLUMED to analyze trajectories. In order to do so, we will
-learn how to use the \ref driver tool.
-Let's look at the options of PLUMED \ref driver by issuing the following command:
+Now we can create a conda environment for the ISDD tutorial using the following commands:
\verbatim
-plumed driver --help
+# create environment
+conda create --name ISDD-tutorial-2021
\endverbatim
-As you can see we can do a number of things with PLUMED \ref driver. For all of these options, however, we are going to need to write
-a PLUMED input file. The syntax of the PLUMED input file is the same that we will use later to run enhanced sampling simulations during
-a MD simulation, so all the things that you will learn now will be useful later when you will run PLUMED coupled to GROMACS.
-
-\subsection master-ISDD-1-gromacs GROMACS
-
-GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.
-More info can be found <a href="http://www.gromacs.org">here</a>.
-
-To be able to use GROMACS on your machine, you need to execute the following command line in your bash terminal:
+and activate it with:
\verbatim
-source /opt/sdv/gromacs-2019.6/bin/GMXRC
+# activate environment
+conda activate ISDD-tutorial-2021
\endverbatim
-You need to execute the command above in every new terminal window (shell) you open. Alternatively, you can add the line
-to the file `.bashrc` located in your home directory. After doing this, you can open a new shell and check that GROMACS is properly working by typing:
+Finally, we can proceed with the installation of the required software:
\verbatim
-gmx mdrun -h
+conda install -c conda-forge plumed py-plumed
+conda install --strict-channel-priority -c plumed/label/masterclass -c conda-forge gromacs
\endverbatim
-If you inspect the long output generated by this command, you will notice a `-plumed` option, which indicates that GROMACS has
-properly been compiled with PLUMED. Great, now you are ready to go!
+The `--strict-channel-priority` might be necessary in case your conda install is configured to download packages from the `bioconda` channel. Indeed, `bioconda` contains a version of GROMACS that is **not** patched with PLUMED and would thus not work here.
-\hidden{Install GROMACS+PLUMED on your own machine with Conda}
+Keep in mind that every time you open a new shell, in order to use PLUMED and GROMACS you need to
+activate the `ISDD-tutorial-2021` Conda environment using the following command:
-In the eventuality in which you cannot find the software on your machine or you are working remotely, you can find a pre-compiled
-version of GROMACS 2018.8 patched with PLUMED version 2.6.2 on Conda.
+\verbatim
+conda activate ISDD-tutorial-2021
+\endverbatim
-First, check if Conda is installed on your machine by typing:
+\subsection master-ISDD-1-plumed PLUMED overview
+
+PLUMED is a library that can be incorporated into many MD codes by adding a relatively simple and well documented interface.
+Once it is incorporated you can use PLUMED to perform a variety of different analyses on-the-fly and to bias
+the sampling in MD simulations. Additionally, PLUMED can be used as a standalone code for analyzing trajectories.
+If you are using the code in this way you can run the PLUMED executable by issuing the command:
\verbatim
-conda
+plumed <instructions>
\endverbatim
-In case the command is not found, please follow the instructions below to install Conda in the
-directory `/path/to/conda`. You can choose it in your home so that you will have write permission to it.
+Let's start by getting a feel for the range of calculations that PLUMED can do. Issue the following command now:
\verbatim
-# on Linux:
-wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-# on MacOS:
-# wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
-bash ./miniconda.sh -b -f -p /path/to/conda
-# export PATH to find the Conda executable
-export PATH="/path/to/conda/bin:$PATH"
-# initialize bash shell
-conda init bash
+plumed --help
\endverbatim
-Now you can open a new shell and create a separate environment for the ISDD tutorial using the following commands:
+The output of this command is a list of tasks that PLUMED can perform. Among these, there are commands that allow you
+to patch an MD code, postprocess metadynamics simulations, and build the manual. In this
+tutorial we will mostly use PLUMED to analyze trajectories. In order to do so, we will
+learn how to use the \ref driver tool.
+Let's look at the options of PLUMED \ref driver by issuing the following command:
\verbatim
-# create environment
-conda create --name ISDD-tutorial
-# activate environment
-conda activate ISDD-tutorial
+plumed driver --help
\endverbatim
-Finally, you can install the pre-compiled version of GROMACS 2018.8 patched with PLUMED 2.6.2:
+As you can see we can do a number of things with PLUMED \ref driver. For all of these options, however, we are going to need to write
+a PLUMED input file. The syntax of the PLUMED input file is the same that we will use later to run enhanced sampling simulations during
+a MD simulation, so all the things that you will learn now will be useful later when you will run PLUMED coupled to GROMACS.
-\verbatim
-conda install -c plumed/label/munster -c conda-forge gromacs
-\endverbatim
+\subsection master-ISDD-1-gromacs GROMACS overview
-and check your installation by typing:
+GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.
+More info can be found <a href="http://www.gromacs.org">here</a>.
+
+You can check that GROMACS is properly working by typing:
\verbatim
gmx mdrun -h
@@ -125,15 +121,6 @@ gmx mdrun -h
If you inspect the long output generated by this command, you will notice a `-plumed` option, which indicates that GROMACS has
properly been compiled with PLUMED. Great, now you are ready to go!
-Keep in mind that every time you open a new shell, in order to use PLUMED and GROMACS you need to
-activate the `ISDD-tutorial` Conda environment using the following command:
-
-\verbatim
-conda activate ISDD-tutorial
-\endverbatim
-
-\endhidden
-
\section master-ISDD-1-structure Your first PLUMED input file
The main goal of PLUMED is to compute collective variables (or CVs), which are complex descriptors
diff --git a/user-doc/tutorials/aa-master-ISDD-2.txt b/user-doc/tutorials/aa-master-ISDD-2.txt
index 5b5e5bd8f..6f10d2df2 100644
--- a/user-doc/tutorials/aa-master-ISDD-2.txt
+++ b/user-doc/tutorials/aa-master-ISDD-2.txt
@@ -1,14 +1,14 @@
/**
-\page master-ISDD-2 Master ISDD tutorial 2020: Metadynamics simulations with PLUMED
+\page master-ISDD-2 Master ISDD tutorial 2021: Metadynamics simulations with PLUMED
\section master-ISDD-2-aims Aims
The aim of this tutorial is to train users to perform and analyze 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.
+at Universite' de Paris on October 26th, 2021.
-\section master-ISDD-2-objectives Learning Outcomes
+\section master-ISDD-2-objectives Aims
Once this tutorial is completed users will be able to:
--
GitLab