.. _user-guide-getting-started: .. role:: header :class: h4 Getting started with |pyretis| ============================== After :ref:`installing PyRETIS `, you can run simulations by using a **text based input file** or by using **the PyRETIS library explicitly**. The former approach is perhaps the simplest, but you will first have to learn how to create input files and this is explained in the :ref:`input description `. The latter option is more involved, but you are then given more freedom in defining, running and interacting with a simulation. In order to make use of the library, you will have to read about the structure of the |pyretis| library in the :ref:`introduction to the library ` and in the :ref:`detailed reference section `. A more extensive overview can be found in the :ref:`full user guide `. Since version 2.4, |pyvisa| is automatically installed with |pyretis|. Here, we report some examples showing the use of |pyretis| and |pyvisa|. | |pyretis| examples ------------------ In addition to reading the documentation, we have prepared several examples to highlight the usage and capabilities of |pyretis|. The full list of examples can be found in the :ref:`example section `. .. container:: row .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/md-nve.png :width: 100% :class: img-responsive :target: ../examples/examples-md.html .. container:: caption :header:`Molecular dynamics` In this example, we simply run a MD simulation. This is just intended as an example of how one can make use of |pyretis| as a library. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/tis-1d-pot.png :width: 100% :class: img-responsive :target: ../examples/examples-tis-1d.html .. container:: caption :header:`TIS` This example shows how we can run a Transition Interface Sampling calculation and obtain a crossing probability. Here, we consider a 1D potential in which a single particle is moving. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/retis-1d-pot.png :width: 100% :class: img-responsive :target: ../examples/examples-retis-1d.html .. container:: caption :header:`RETIS` This example show how we can run a Replica Exchange Transition Interface Sampling calculation and obtain a crossing probability and a rate constant. Here, we consider a 1D potential in which a single particle is moving. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/2dpot.png :width: 100% :class: img-responsive :target: ../examples/examples-2d-hysteresis.html .. container:: caption :header:`RETIS 2D` In this example, we perform a simulation of a 2D potential which is constructed such that the selection of the order parameter is not so obvious. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/pyretisrev.png :width: 100% :class: img-responsive :target: ../examples/examples-md-fb.html .. container:: caption :header:`Extending with C/FORTRAN` This example shows how we can use FORTRAN or C to speed up |pyretis| calculations. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: http://openmm.org/img/logos/Icon.svg :width: 94% :class: img-responsive :target: ../examples/examples-openmm.html .. container:: caption :header:`Using OpenMM` This example demonstrates how we interface between OpenMM and |pyretis| internal code. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/retis-2d-wca.png :width: 100% :class: img-responsive :target: ../examples/examples-retis-wca.html .. container:: caption :header:`RETIS 2D WCA` Here we calculate the rate for the breaking of a bond between two particles in a fluid. We consider two cases: a low barrier and a high barrier case and we implement the force field in C. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/hydrogen.png :width: 100% :class: img-responsive :target: ../examples/examples-cp2k-hydrogen.html .. container:: caption :header:`Using CP2K` This example demonstrates how we can make use of CP2K for running the dynamics for |pyretis|. Here, we are just studying a toy example - breakage of the bond in hydrogen. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/hydrate.png :width: 100% :class: img-responsive :target: ../examples/examples-gromacs-hydrate.html .. container:: caption :header:`Using GROMACS` This example demonstrates how we can make use of GROMACS for running the dynamics for |pyretis|. In this particular example, we study the diffusion of methane in a sI hydrate structure. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/2d-lammps.png :width: 100% :class: img-responsive :target: ../examples/examples-lammps-wca.html .. container:: caption :header:`Using LAMMPS` This example demonstrates how we can make use of LAMMPS for running the dynamics for |pyretis|. In this particular example, we revisit the 2D WCA example and use LAMMPS as our molecular dynamics engine. .. container:: col-lg-3 col-md-3 col-sm-3 col-xs-6 thumbnail thumbnail2 .. image:: /_static/img/examples/thumbnails/contour-400x400.png :width: 100% :class: img-responsive :target: ../examples/examples-pyvisa.html .. container:: caption :header:`PyVisA` In this example, we show the usage of |pyvisa|. First, the optional requisite, PyQt5, is installed to enable |pyvisa| GUI. The compressor tool, and the visualization tool usage is then demostrated. A few sample pictures are reported. | Main studies performed with |pyretis| ------------------------------------- .. container:: row .. container:: col-lg-4 col-md-4 col-sm-4 col-xs-6 thumbnail thumbnail3 .. image:: /_static/img/examples/thumbnails/dna-400x400.png :width: 100% :class: img-responsive .. container:: caption :header:`Predicting the mechanism and rate of H-NS binding to AT-rich DNA.` The adsorption of H-NS on DNA is studied at atomistic resolution with GROMACS. Local minima have been located by metadynamics and the transition rates computed by RETIS. Paper: `Predicting the mechanism and rate of H-NS binding to AT-rich DNA `_ `Source Files `__ .. container:: col-lg-4 col-md-4 col-sm-4 col-xs-6 thumbnail thumbnail3 .. image:: /_static/img/examples/thumbnails/water-400x400.png :width: 100% :class: img-responsive .. container:: caption :header:`Autoionization of water.` BO-DFT simulations, via the RETIS approach, were used to study water autoionization. The mechanism(s) have been highlighted and their rate(s) quantified. Machine learning was applied to test the quality of the order parameters. Paper: `Local initiation conditions for water autoionization `_ `Source Files `__ .. container:: col-lg-4 col-md-4 col-sm-4 col-xs-6 thumbnail thumbnail3 .. image:: /_static/img/examples/thumbnails/cyclophilin-400x400.png :width: 100% :class: img-responsive .. container:: caption :header:`Conformational study of Cyclophilin - A.` Full atomistic simulations with GROMACS have been performed to sample and quantify the rate of the structural rearrangements of CyP-A and its muted confomer. Paper in preparation. `Source Files `__ .. container:: col-lg-4 col-md-4 col-sm-4 col-xs-6 thumbnail thumbnail3 .. image:: /_static/img/examples/thumbnails/trimer-400x400.png :width: 100% :class: img-responsive .. container:: caption :header:`Proton transfer in a water trimer.` A study on the proton transfer reaction with a polarizable potential is included. The various features of |pyvisa| can be tested on the simulation outputs. Paper in preparation. `Source Files `__ .. container:: col-lg-4 col-md-4 col-sm-4 col-xs-6 thumbnail thumbnail3 .. image:: /_static/img/examples/thumbnails/formic-400x400.png :width: 100% :class: img-responsive .. container:: caption :header:`Formic acid catalysed formation of sulfuric acid`. A study on the formic acid catalysed conversion of sulfur trioxide and water to sulfuric acid. The mechanism(s) have been highlighted and their rate(s) estimated as a function of the temperature. Paper: `Path sampling for atmospheric reactions: formic acid catalysed conversion `_ `Source Files `__