Sometimes it is convenient to read the COLVAR file (Plumed output) using pandas as it can act as a first step for machine learning based data analysis e.g. time-series forecasting, clustering, dimensionality […]
bhakatsoumendranath
Reweighting Metadynamics
In my last post I described how to check convergence of metadynamics simulation. However, the 1D free energy surface showed in the previous post is not reweighted and corrected properly because I […]
Convergence of Metadynamics simulation
Convergence of metadynamics or any enhanced sampling calculations plays an important role in deciding how much you can trust the outcomes from metadynamics simulations. here is a step by step tutorial and […]
tICA Metadynamics
Time-lagged independent component analysis is a dimensionality reduction technique which transforms a high dimensional dataset to lower dimensional co-ordinates. It’s philosophy is kind of similar to PCA (principal component analysis). For more […]
Parameter for zinc centre proteins
Parametrization of metallo-proteins always been a challenging problem during the set-up of classical molecular dynamics simulation. This tutorial will describe a short-cut way to set up and Zinc (Zn2+) co-ordinated metallo-protein where […]
Possible new idea with tSNE
Dimensionality reduction is in the hurt of molecular dynamics simulations keeping in mind its importance in reducing the high-dimension data produced during molecular dynamics simulations. It also found application in building Markov […]
Analysis of MD trajectory using tSNE
Before starting anything with tSNE let’s read what is tSNE and how it has been compared with PCA. You can read it here. Several implementations of t-SNE are available here. A great introductory […]
Jupyter notebook and Matplotlib
I was thinking to use Jupyter notebook for quite a some time and finally I started using it. Here is a quick installation guide for Linux (Ubuntu). If Python is already installed […]
Useful scripts
Disclaimer: All these scripts were written by Emil Åberg Imagine you have multiple folders with rec.pdbqt and rec.pdb files and have a folder with all the ligands with .pdbqt files. Imagine now […]
Modelling of ZIKA proteases
Disclaimer: This blog is made public in order to inspire a new generation of enthusiastic people to start working on this neglected disease as soon as possible. I was doing some side-project […]
