From 2d8ee712aabdf3d9c6e554e4990c473fd61db5a0 Mon Sep 17 00:00:00 2001 From: James Krieger Date: Fri, 8 Aug 2025 14:48:38 +0100 Subject: [PATCH 1/4] Update README.md for broken gromacs install link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index abc569b..fede22b 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ The main point is to enable Libtorch with: ## **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** From 1477ea5d313055d2af11e10bfc531475dbc20990 Mon Sep 17 00:00:00 2001 From: James Krieger Date: Thu, 14 Aug 2025 11:08:42 +0100 Subject: [PATCH 2/4] another broken link fix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fede22b..579c80e 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ 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` From 025716c973fb2f5857165a7be3a1b4737278ddb7 Mon Sep 17 00:00:00 2001 From: James Krieger Date: Thu, 14 Aug 2025 11:10:13 +0100 Subject: [PATCH 3/4] another broken link fix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 579c80e..2c1cec7 100644 --- a/README.md +++ b/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](https://github.com/COSBlab/EMMIVox/tree/main/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** From 45a53fd9291cbc4382485a9762335f7a7e514a15 Mon Sep 17 00:00:00 2001 From: James Krieger Date: Thu, 14 Aug 2025 18:42:42 +0100 Subject: [PATCH 4/4] add relative links --- README.md | 2 +- tutorials/1-refinement/README.md | 4 ++-- tutorials/3-refinement-wat/README.md | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 2c1cec7..ba543b0 100644 --- a/README.md +++ b/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/COSBlab/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** diff --git a/tutorials/1-refinement/README.md b/tutorials/1-refinement/README.md index f252521..7fda49a 100644 --- a/tutorials/1-refinement/README.md +++ b/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` diff --git a/tutorials/3-refinement-wat/README.md b/tutorials/3-refinement-wat/README.md index b079219..ea38336 100644 --- a/tutorials/3-refinement-wat/README.md +++ b/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`: