.. hymd documentation master file, created by sphinx-quickstart on Thu Dec 16 13:31:43 2021. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ############################### HylleraasMD documentation ############################### :Release: |release| :Date: |today| **HylleraasMD** (HyMD) is a massively parallel Python package for hybrid particle-field molecular dynamics (hPF-MD) simulations of coarse-grained bio- and soft-matter systems. HyMD can run canonical hPF-MD simulations :cite:`Milano2009JCP`, or filtered density Hamiltonian hPF (HhPF-MD) simulations :cite:`bore2020hamiltonian`, with or without explicit PME electrostatic interactions :cite:`kolli2018JCTC`. 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 :cite:`Cascella2008,bore2018hybrid`. Martini style elastic networks (ElNeDyn) :cite:`periole2009combining` are also supported. HyMD uses the pmesh (`github.com/rainwoodman/pmesh`_) library for particle-mesh operations, with the PPFT :cite:`pippig2013pfft` backend for FFTs through the pfft-python bindings (`github.com/rainwoodman/pfft-python`_). File IO is done via HDF5 formats to allow MPI parallel reads. User Guide ========== The HylleraasMD :doc:`User Guide ` provides comprehensive information on how to run simulations. Selected :doc:`Examples ` are available to guide new users. .. _`github.com/rainwoodman/pmesh`: https://github.com/rainwoodman/pmesh .. _`github.com/rainwoodman/pfft-python`: https://github.com/rainwoodman/pfft-python Installing HyMD =============== The easiest approach is to install using pip_: .. code-block:: bash 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`. .. _pip: http://www.pip-installer.org/en/latest/index.html Run in Google colab ------------------- Run HyMD interactively in `Google Colaboratory`_ jupyter notebook `here`_. .. _`Google colaboratory` : https://colab.research.google.com/ .. _`here` : https://colab.research.google.com/drive/1jfzRaXjL3q53J4U8OrCgADepmf_HuCOh?usp=sharing 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`_: .. code-block:: bash git clone https://github.com/Cascella-Group-UiO/HyMD.git .. _GNU Lesser General Public License v3.0: https://www.gnu.org/licenses/lgpl-3.0.html .. _git: https://git-scm.com/ Development =========== HyMD is developed and maintained by researchers at the `Hylleraas Centre for Quantum Molecular Sciences`_ at the `University of Oslo`_. |pic1| |pic2| .. _`Hylleraas Centre for Quantum Molecular Sciences`: https://www.mn.uio.no/hylleraas/english/ .. _`University of Oslo`: https://www.uio.no/ .. |pic1| image:: img/hylleraas_centre_logo_black.png :target: img/hylleraas_centre_logo_black.png :width: 250 px .. |pic2| image:: img/uio_full_logo_eng_pos.png :target: img/uio_full_logo_eng_pos.png :width: 325 px References ========== .. bibliography:: :all: Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` .. Contents .. ======== .. 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 .. toctree:: :maxdepth: 2 :numbered: :hidden: :caption: Developer documentation ./doc_pages/interaction_energy_functionals ./doc_pages/filtering ./doc_pages/benchmarks ./doc_pages/api