In my last post I described how to check convergence of metadynamics simulation. However, the 1D free energy surface showed … More
Author: bhakatsoumendranath
Convergence of Metadynamics simulation
Convergence of metadynamics or any enhanced sampling calculations plays an important role in deciding how much you can trust the … More
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 … 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 … More
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 … More
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 … More
Jupyter notebook and Matplotlib
I was thinking to use Jupyter notebook for quite a some time and finally I started using it. Here is … More
Useful scripts
Disclaimer: All these scripts were written by Emil Åberg Imagine you have multiple folders with rec.pdbqt and rec.pdb files and … More
Modelling of ZIKA proteases
Disclaimer: This blog is made public in order to inspire a new generation of enthusiastic people to start working on … More
New review on “Flap Dynamics”
Our latest review deals with computational study on “Flap dynamics” across proteases has been accepted in Chemical Biology & Drug … More
