Update README.md for broken links

README.md

@@ -18,7 +18,7 @@ This repository is organized in the following two directories:
  * MPI library/compilers for multi-replica ensemble simulations.
  * Cuda, needed by both GROMACS and PLUMED. The exact version depends a bit on how old your GPUs are.
  * [LibTorch](https://pytorch.org/get-started/locally/). Make sure you download the C++ version (LibTorch, not pytorch) that is supported by the Cuda version you installed; 
- * Conda to install the python libraries needed by the pre- and post-processing scripts. Have a look [here](https://github.com/maxbonomi/EMMIVox/tree/main/scripts) for more info about the libraries that you need to install.
+ * Conda to install the python libraries needed by the pre- and post-processing scripts. Have a look [here](scripts) for more info about the libraries that you need to install.
  * [Phenix](https://phenix-online.org/documentation/index.html) (any recent version), if you want to validate single-structure refinement. Not really needed for ensemble modelling.
 
 ## **PLUMED installation**
@@ -35,14 +35,14 @@ or downloading the following zip archive:
 
 ### 2. Configuring and compiling PLUMED
 
-Please have a look [here](https://www.plumed.org/doc-master/user-doc/html/_i_s_d_b.html) for detailed instructions about compiling PLUMED with Libtorch support.
+Please have a look [here](https://www.plumed.org/doc-master/user-doc/html/module_isdb/) for detailed instructions about compiling PLUMED with Libtorch support.
 The main point is to enable Libtorch with:
 
 `./configure --enable-libtorch`
 
 ## **GROMACS installation**
 
-Detailed instructions about patching GROMACS with PLUMED, configuration and installation are available [here](https://www.plumed.org/doc-master/user-doc/html/_installation.html).
+Detailed instructions about patching GROMACS with PLUMED, configuration and installation are available [here](https://www.plumed-tutorials.org/lessons/20/001/data/gromacs.html).
 
 ## **Credits and contact**
 

tutorials/1-refinement/README.md

@@ -2,7 +2,7 @@
 These are the steps for refining a single structural model into a cryo-EM maps with EMMIVox.
 Each step of the procedure will be carried out in a separate directory.
 
-**Note**: all the python scripts are contained in [`scripts`](https://github.com/maxbonomi/EMMIVox/tree/main/scripts).
+**Note**: all the python scripts are contained in [`scripts`](../../scripts/).
 
 ## 0. System setup
 
@@ -18,7 +18,7 @@ Each step of the procedure will be carried out in a separate directory.
 
    * Add to the index file created by CHARMM-GUI (`index.ndx`) two custom groups:
 
-     * `System-MAP`, which contains all the atoms that will be used to generate the cryo-EM map. You can do this with `make_ndx.py` in [`scripts`](https://github.com/maxbonomi/EMMIVox/tree/main/scripts) using [`MDAnalysis`](https://www.mdanalysis.org) selection syntax. Hydrogen atoms and the carboxylate oxygens of glutamic/aspartic acid will be automatically removed from this group, as they are not used in PLUMED to calculate the cryo-EM map. A second group, called `System-MAP-H` will also be created to include these missing atoms (mostly to write them in the trajectory file).
+     * `System-MAP`, which contains all the atoms that will be used to generate the cryo-EM map. You can do this with `make_ndx.py` in [`scripts`](../../scripts/) using [`MDAnalysis`](https://www.mdanalysis.org) selection syntax. Hydrogen atoms and the carboxylate oxygens of glutamic/aspartic acid will be automatically removed from this group, as they are not used in PLUMED to calculate the cryo-EM map. A second group, called `System-MAP-H` will also be created to include these missing atoms (mostly to write them in the trajectory file).
 
         `python make_ndx.py step3_input.gro "protein" System-MAP --ndx index.ndx`
 

tutorials/3-refinement-wat/README.md

@@ -2,7 +2,7 @@
 These are the steps for refining a single structural model into a cryo-EM maps with EMMIVox.
 Each step of the procedure will be carried out in a separate directory.
 
-**Note**: all the python scripts are contained in [`scripts`](https://github.com/maxbonomi/EMMIVox/tree/main/scripts).
+**Note**: all the python scripts are contained in [`scripts`](../../scripts/).
 
 ## 0. System setup
 
@@ -16,7 +16,7 @@ Each step of the procedure will be carried out in a separate directory.
 
      `bash renumber.sh step3_input.gro step3_input.pdb`
 
-   * Add the following custom groups to the index file created by CHARMM-GUI (`index.ndx`). You can create them with `make_ndx.py` in [`scripts`](https://github.com/maxbonomi/EMMIVox/tree/main/scripts) using [MDAnalysis](https://www.mdanalysis.org) selection syntax:
+   * Add the following custom groups to the index file created by CHARMM-GUI (`index.ndx`). You can create them with `make_ndx.py` in [`scripts`](../../scripts/) using [MDAnalysis](https://www.mdanalysis.org) selection syntax:
 
        * `System-WAT`: the ordered waters (residues 380-455) and a water buffer of 3.5 Ang around them.
           Waters require a special treatment when building the `index.ndx` file, therefore we need to use the flag `--water`: