PLUMED-ISDB

Overview

The ISDB module contains collective variables, functions and biases originally developed for Integrative Structural and Dynamical Biology. They are related but not limited to the interpretation and modelling of experimental data in molecular modelling.

Some of the functionalities implemented in the ISDB module require the PyTorch C++ APIs (LibTorch) to be linked against PLUMED. Currently, these include:

• EMMIVOX

To activate these functionalities, please follow the installation instructions below.

Installation

To compile PLUMED with LibTorch support, please look at the installation instruction about LibTorch. It is highly recommened to install the CUDA version of LibTorch to calculate EMMIVOX efficiently on the GPU.

Once LibTorch has been downloaded and the relevant environment variables are set, one can configure PLUMED with the following options:

> ./configure --enable-libtorch

Warning

Libtorch APIs are still in beta phase regarding stability, so there might be breaking changes in newer versions. Currently, versions of LibTorch between 1.8.* and 2.0.0 have been tested.

Usage

• CVs Documentation
• Functions Documentation
• General Actions Documentation
• Biases Documentation

Additional tutorials focused on the ISDB module are included in the following and are meant as advanced tutorials.

• Tutorials