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###############
About |pyretis|
###############

|pyretis| is a `Python <https://www.python.org>`_ library
for **rare event molecular simulations**
with emphasis on methods based on
:ref:`transition interface sampling <user-guide-tis-theory>`
and :ref:`replica exchange transition interface sampling <user-guide-retis-theory>`.
The papers describing the |pyretis| program
can be found here: `<https://doi.org/10.1002/jcc.24900>`_ (|pyretis| 1, 2017),
here: `<https://doi.org/10.1002/jcc.26112>`_ (|pyretis| 2, 2020),
and here: `<https://doi.org/10.1002/jcc.27319>`_ (|pyretis| 3, 2024).

The work on |pyretis| was initiated by `Titus van Erp <http://www.van-erp.org>`_ and is used in
the research and teaching activities in the
`theoretical chemistry <http://www.ntnu.edu/chemistry/research/theoretical-chemistry>`_
group at the `Norwegian University of Science and Technology <http://www.ntnu.edu/>`_.

|pyretis| is open source and is released
under a :ref:`GNU Lesser General Public license v2.1+ <pyretis-license>`.
If you are interested in contributing to the |pyretis| project,
please have a look
at the :ref:`developer guide <developer-guide-index>` and visit our
git repository `<https://gitlab.com/pyretis/pyretis>`_.

The current |pyretis| version is |version|.
For an overview of the official |pyretis| releases,
please visit our git repository: `<https://gitlab.com/pyretis/pyretis/-/releases>`_.

Since version 2.4, |pyretis| includes |pyvisa|, a program created to
facilitate post-processing and data analysis.


The |pyretis| team
------------------

**Head authors & project leaders:**

* `Titus van Erp <https://www.ntnu.edu/employees/titus.van.erp>`__

* `Enrico Riccardi <https://www.uis.no/nb/profile/enrico-riccardi>`_


**Developers:**

* `Arthur Benigno Weidmann <https://portal.dados.unicamp.br/perfil?docente=330260>`_

* `Jonas Jaeger <https://www.uis.no/nb/profile/jonas-jaeger>`_

* `Dinis O. Abranches <https://www.ciceco.ua.pt/?tabela=pessoaldetail&menu=219&user=1903>`_

**Former Developers:**

* `An Ghysels <https://www.ugent.be/ea/ibitech/en/about-us/biommeda-staff-1/professor-an-ghysels.htm>`_

* `Daniel Tianhou Zhang <https://www.linkedin.com/in/daniel-tianhou-zhang-857545192>`_

* `Ola Aarøen <https://www.linkedin.com/in/ola-aar%C3%B8en-64023678>`_

* `Sander Roet  <https://www.linkedin.com/in/sander-roet>`_

* `Anders Lervik <https://www.ntnu.edu/employees/anders.lervik>`_


**Acknowledgments:**

* `Wouter Vervust <https://www.ugent.be/ea/ibitech/en/about-us/biommeda-staff-1/ir-wouter-vervust.htm>`_

* `Henrik Kiær <https://www.linkedin.com/in/henrikkiaer/?originalSubdomain=no>`_

* `Anastasia Maslechko <https://www.linkedin.com/in/anastasia-maslechko-87207b95/?originalSubdomain=ua>`_

* Oda Dahlen

* Christopher Daub

* Mahmoud Moqadam

* César A. Urbina-Blanco 

* Jocelyne Vreede

* Magnus Heskestad Waage

* `Sudi Jawahery <https://www.linkedin.com/in/sudi-jawahery-78559b37>`_

* `Raffaela Cabriolu <https://www.linkedin.com/in/raffaela-cabriolu-41ba5488/?originalSubdomain=it>`_


|

To cite us:
-----------

When using |pyretis|, or one of our libraries, please cite us!

**Software papers:**

* A. Lervik, E. Riccardi and T. S. van Erp, `PyRETIS: A well-done,
  medium-sized python library for rare events
  <https://doi.org/10.1002/jcc.24900>`_, J. Comput. Chem. **38**,
  2439-2451 (2017).

* E. Riccardi, A. Lervik, S. Roet, O. Aarøen and T. S. van Erp,
  `PyRETIS 2: An improbability drive for rare events
  <https://doi.org/10.1002/jcc.26112>`_, J. Comput. Chem. **41**,
  370-377 (2020).

* O. Aarøen, H. Kiær and E. Riccardi, `PyVisA: Visualization and
  Analysis of path sampling trajectories
  <https://doi.org/10.1002/jcc.26467>`_, J. Comput. Chem. **42**,
  435-446 (2021).

* W. Vervust, D. T. Zhang, A. Ghysels, S. Roet, T. S. van Erp and
  E. Riccardi, `PyRETIS 3: Conquering rare and slow events without
  boundaries <https://doi.org/10.1002/jcc.27319>`_, J. Comput. Chem.
  **45**, 1224-1234 (2024).


**Studies based on PyRETIS:**

In addition to the software papers above, the following published
studies use |pyretis| or |pyvisa| to sample, analyse or visualise rare
events.  They include work by members of our group and by other authors
building on the software.

* T. S. van Erp, M. Moqadam, E. Riccardi and A. Lervik, `Analyzing
  complex reaction mechanisms using path sampling
  <https://doi.org/10.1021/acs.jctc.6b00642>`_, J. Chem. Theory Comput.
  **12**, 5398-5410 (2016).

* M. Moqadam, E. Riccardi, T. T. Trinh, A. Lervik and T. S. van Erp,
  `Rare event simulations reveal subtle key steps in aqueous silicate
  condensation <https://doi.org/10.1039/C7CP01268C>`_,
  Phys. Chem. Chem. Phys. **19**, 13361-13371 (2017).

* E. Riccardi, O. Dahlen and T. S. van Erp, `Fast decorrelating Monte
  Carlo moves for efficient path sampling
  <https://doi.org/10.1021/acs.jpclett.7b01617>`_, J. Phys. Chem. Lett.
  **8**, 4456-4460 (2017).

* M. Moqadam, A. Lervik, E. Riccardi, V. Venkatraman, B. K. Alsberg
  and T. S. van Erp, `Local initiation conditions for water
  autoionization <https://doi.org/10.1073/pnas.1714070115>`_,
  Proc. Natl. Acad. Sci. U.S.A. **115**, E4569-E4576 (2018).

* E. Riccardi, E. C. van Mastbergen, W. W. Navarre and J. Vreede,
  `Predicting the mechanism and rate of H-NS binding to AT-rich DNA
  <https://doi.org/10.1371/journal.pcbi.1006845>`_, PLoS Comput. Biol.
  **15**, e1006845 (2019).

* C. D. Daub, E. Riccardi, V. Hänninen and L. Halonen, `Path sampling
  for atmospheric reactions: formic acid catalysed conversion of SO3 + H2O
  to H2SO4 <https://doi.org/10.7717/peerj-pchem.7>`_,
  PeerJ Phys. Chem. **2**, e7 (2020).

* E. Riccardi, A. Krämer, T. S. van Erp and A. Ghysels, `Permeation
  rates of oxygen through a lipid bilayer using replica exchange
  transition interface sampling <https://doi.org/10.1021/acs.jpcb.0c09947>`_,
  J. Phys. Chem. B **125**, 193-201 (2021).

* S. Roet, C. D. Daub and E. Riccardi, `Chemistrees: Data-Driven
  Identification of Reaction Pathways via Machine Learning
  <https://doi.org/10.1021/acs.jctc.1c00458>`_,
  J. Chem. Theory Comput. **17**, 6193-6202 (2021).

* A. Lervik, I.-H. Svenum, Z. Wang, R. Cabriolu, E. Riccardi,
  S. Andersson and T. S. van Erp, `The role of pressure and defects in
  the wurtzite to rock salt transition in cadmium selenide
  <https://doi.org/10.1039/d1cp05051f>`_, Phys. Chem. Chem. Phys.
  **24**, 8378-8386 (2022).

* D. T. Zhang, E. Riccardi and T. S. van Erp, `Enhanced path sampling
  using subtrajectory Monte Carlo moves <https://doi.org/10.1063/5.0127249>`_,
  J. Chem. Phys. **158**, 024113 (2023).

* V. Munizaga and M. L. Falk, `The thermodynamic effects of solute on
  void nucleation in Mg alloys <https://doi.org/10.1063/5.0196513>`_,
  J. Chem. Phys. **161**, 044509 (2024).

* K. Wilke, S. Tao, S. Calero, A. Lervik and T. S. van Erp, `NaCl
  dissociation explored through predictive power path sampling analysis
  <https://doi.org/10.1021/acs.jctc.5c00054>`_, J. Chem. Theory Comput.
  **21**, 4604-4614 (2025).

* W. Vervust, D. T. Zhang, E. Riccardi, T. S. van Erp and A. Ghysels,
  `Path sampling challenges in large biomolecular systems: RETIS and
  REPPTIS for ABL-imatinib kinetics
  <https://doi.org/10.1016/j.bpj.2025.04.020>`_, Biophys. J. **124**,
  3932-3947 (2025).


**Additional theory papers from our group:**

* T. S. van Erp, D. Moroni and P. G. Bolhuis, `A novel path sampling
  method for the calculation of rate constants
  <https://doi.org/10.1063/1.1562614>`_, J. Chem. Phys. **118**,
  7762-7774 (2003).

* T. S. van Erp, `Reaction rate calculation by parallel path swapping
  <https://doi.org/10.1103/PhysRevLett.98.268301>`_, Phys. Rev. Lett.
  **98**, 268301 (2007).

* A. Ghysels, S. Roet, S. Davoudi and T. S. van Erp, `Exact
  non-Markovian permeability from rare event simulations
  <https://doi.org/10.1103/PhysRevResearch.3.033068>`_, Phys. Rev.
  Res. **3**, 033068 (2021).

* W. Vervust, D. T. Zhang, T. S. van Erp and A. Ghysels,
  `Path sampling with memory reduction and replica exchange to reach
  long permeation timescales <https://doi.org/10.1016/j.bpj.2023.02.021>`_,
  Biophys. J. **122**, 2960-2972 (2023).

* D. T. Zhang, L. Baldauf, S. Roet, A. Lervik and T. S. van Erp,
  `Highly parallelizable path sampling with minimal rejections using
  asynchronous replica exchange and infinite swaps
  <https://doi.org/10.1073/pnas.2318731121>`_, Proc. Natl. Acad. Sci.
  U.S.A. **121**, e2318731121 (2024).