Commit 767d2aa7 authored by Alan O'Cais's avatar Alan O'Cais
Browse files

Update readme.rst

parent 6bc786e9
Pipeline #8371 passed with stages
in 2 minutes and 25 seconds
********************************************************************************
########################
Comparative Metadynamics
********************************************************************************
########################
.. sidebar:: Software Technical information
......@@ -29,17 +29,15 @@ Comparative Metadynamics
.. contents:: :local:
********
Abstract
********
________
The module performs a long simulation of some given system and then many shorter simulations of mutations of the
aforementioned system. Using the Free Energy Surface (FES) of the original system as a basepoint allows for meaningful
information about the impact of a mutation on the system's FES to be extracted from only the short simulations.
**********************
Background Information
**********************
______________________
The use of Molecular Dynamics (MD) is highly relevant in nearly all STEM fields. Analysing MD simulations can be done
by defining Collective Variables (CVs), functions of the positions of some or all of the atoms in a simulation. Then,
......@@ -59,9 +57,8 @@ three steps, which are usually repeated many times.
2. Simulating through Metadynamics
3. Analysing the FES
*****************
Purpose of Module
*****************
_________________
The purpose of this module is to speed up the process of optimisation through mutation by quickly classifying roughly
how much a mutation will optimise the system or not. This quick classification will allow a much wider exploration of
......@@ -85,25 +82,24 @@ mutations best optimised the system by comparing which mutations caused the grea
fixed time interval. Thus, this module allows one to test many mutations and narrow down which ones will best optimise
their system.
************
Applications
************
____________
This module is particularly relevant to anywhere MD is being used to design systems through an iterative process such
as chemical or biological labs. However, it can also be applied to areas where one needs to analyse many similar
systems through MD.
***********
Performance
***********
___________
For a simple water in salt system, when changing the charge on the salt ions a simulation time of 100ps was sufficient
to analyse the changes that had occurred in the FES. By contrast a full simulation of the system required at least 4ns
to converge.
**********************
Software Prerequisites
**********************
______________________
The core software requirements are:
1. Python 3
......@@ -121,9 +117,8 @@ additional software is required:
* matplotlib
*****
Usage
*****
_____
All files discussed in this section can be found in the examples folder.
This module mutates a system and then runs a metadynamics simulation of them using lammps. Thus the user needs to
......@@ -160,16 +155,15 @@ A brief summary of what Analyse.ipynb does is provided below
between the max and min value of the FES)
4. Visualises the resulting data
********
Examples
********
~~~~~~~~
`Examples can be found here
<https://gitlab.com/aestheses/comparative-metadynamics/-/tree/master/examples>`_.
***********
Source Code
***********
___________
`Module Source Code <https://gitlab.com/aestheses/comparative-metadynamics>`_
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment