Getting started with PyRETIS
After 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 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
introduction to the library
and in the detailed reference section.
A more extensive overview can be found in
the 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 example section.
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.
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.
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.
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.
Extending with C/FORTRAN
This example shows how we can use FORTRAN or C to speed
up PyRETIS calculations.
Using OpenMM
This example demonstrates how we interface between OpenMM
and PyRETIS internal code.
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.
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.
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.
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.
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
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
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
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