pestifer
========

.. image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.16051498-blue
  :target: https://doi.org/10.5281/zenodo.16051498

.. image:: https://static.pepy.tech/badge/pestifer
   :target: https://pepy.tech/projects/pestifer

**Pestifer** is a versatile system-preparation tool that facilitates the use of the `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ tool `psfgen <https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf>`_ to generate CHARMM-force-field compatible PSF and PDB files for use in the MD simulation package `NAMD <https://www.ks.uiuc.edu/Research/namd/>`_.  Pestifer automates and extends the standard ``psfgen/VMD`` workflow using a simple YAML interface to provide a versatile and user-friendly way to set up molecular dynamics simulations.

Pestifer includes the CHARMM36 force field files from the `MacKerell Lab <https://mackerell.umaryland.edu/charmm_ff.shtml>`_ (February 2026 (default), July 2024 (optional)).  

.. note::

   Pestifer is under active development.  Pestifer development is supported in part by Grants GM100472, AI154071, and AI178833 from the NIH.

Contents
--------

.. toctree::
   :maxdepth: 2

   introduction
   installation
   usage
   examples
   config_ref
   API <api/API>
   Tcl sources <tcl/source>
   Changelog <changelog>