Hardware requirements

To complete this tutorial you need:

A Linux workstation with a multi-core CPU (6-8 cores should be enough);
For ensemble modelling, access to a Linux cluster is preferable;
a GPU to accelerate both the Molecular Dynamics simulation and the calculation of the cryo-EM restraint.

Software requirements

Make sure you have installed:

A modern C++ compiler that supports OpenMP parallelization and C++17.
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. Make sure you download the C++ version (LibTorch, not pytorch) that is supported by the Cuda version you installed;
Phenix (any recent version), if you want to validate single-structure refinement. Not really needed for ensemble modelling.
Conda to install the python libraries needed by the pre- and post-processing scripts: see installation instructions below.
GROMACS and PLUMED: see installation instructions below.
UCSF Chimera or ChimeraX to visualize structural models and cryo-EM density maps.

You can create a conda environment to install all the python libraries needed to run pre- and post-processing tools.

conda create --name emmivox
conda activate emmivox
conda install -c conda-forge mrcfile mdanalysis biopython

Make sure you are installing MDAnalysis version >= 2.0.0.
In this environment, you also need to install pytorch using the instructions available here. Make sure you select a version compatible with the Cuda version installed on your machine or alternatively the CPU version. These instructions are for pytorch version 1.13.0 with Cuda 11.6:

conda install pytorch torchvision torchaudio pytorch-cuda=11.6 -c pytorch -c nvidia

EMMIVox is currently implemented in the GitHub master branch of PLUMED, which you can obtain with:

git clone https://github.com/plumed/plumed2.git

or downloading the following zip archive:

wget https://github.com/plumed/plumed2/archive/refs/heads/master.zip

Please have a look here for detailed instructions about compiling PLUMED with Libtorch support. The main point is to enable Libtorch with:

./configure --enable-libtorch

Detailed instructions about patching GROMACS with PLUMED, configuration and installation are available here.