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HylleraasMD documentation

Release:|release|
Date: |today|

HylleraasMD (HyMD) is a massively parallel Python package for Hamiltonian hybrid particle-field molecular dynamics (HhPF-MD) simulations of coarse-grained bio- and soft-matter systems.

HyMD can run canonical hPF-MD simulations, or filtered density HhPF-MD simulations :cite:`hymd_domain2023,hymd_massive2023,hymd_pressure2023,hymd_alias2020` with or without explicit PME electrostatic interactions. It includes all standard intramolecular interactions, including stretching, bending, torsional, and combined bending-dihedral potentials. Additionally, topological reconstruction of permanent peptide chain backbone dipoles is possible for accurate recreation of protein conformational dynamics. It can run simulations in constant energy (NVE), constant volume (NVT) :cite:`hymd_domain2023,hymd_massive2023` or constant pressure (NPT) conditions :cite:`hymd_pressure2023`. HyMD is also interfaced with :doc:`PLUMED </doc_pages/interfaces>` and can perform simulations using enhanced sampling methods.

HyMD uses the pmesh library for particle-mesh operations, with the PPFT :cite:`pippig2013` backend for FFTs through the pfft-python bindings. File IO is done via HDF5 formats to allow MPI parallel reads.

User Guide

The HylleraasMD :doc:`User Guide </doc_pages/overview>` provides comprehensive information on how to run simulations. Selected :doc:`Examples </doc_pages/examples>` are available to guide new users.

Installing HyMD

The easiest approach is to install using pip:

python3 -m pip install --upgrade pip
python3 -m pip install --upgrade numpy mpi4py cython
python3 -m pip install hymd

For more information and required dependencies, see :ref:`installation-label`.

Run in Google colab

Run HyMD interactively in Google Colaboratory jupyter notebook here.

Source Code

Source code is available from https://github.com/Cascella-Group-UiO/HyMD/ under the GNU Lesser General Public License v3.0. Obtain the source code with git:

git clone https://github.com/Cascella-Group-UiO/HyMD.git

Development

HyMD is developed and maintained by researchers at the Hylleraas Centre for Quantum Molecular Sciences at the University of Oslo.

pic1 pic2

References

.. bibliography::
  :all:

Indices and tables

.. toctree::
   :maxdepth: 2
   :numbered:
   :hidden:
   :caption: Getting started

   ./doc_pages/installation
   ./doc_pages/overview
   ./doc_pages/config_file
   ./doc_pages/topology_input
   ./doc_pages/command_line
   ./doc_pages/constants_and_units



.. toctree::
   :maxdepth: 2
   :numbered:
   :hidden:
   :caption: Examples

   ./doc_pages/examples


.. toctree::
   :maxdepth: 2
   :numbered:
   :hidden:
   :caption: Theory

   ./doc_pages/theory
   ./doc_pages/intramolecular_bonds
   ./doc_pages/electrostatics
   ./doc_pages/pressure
   ./doc_pages/interfaces


.. toctree::
   :maxdepth: 2
   :numbered:
   :hidden:
   :caption: Developer documentation

   ./doc_pages/interaction_energy_functionals
   ./doc_pages/filtering
   ./doc_pages/benchmarks
   ./doc_pages/api