Read COLVAR file using pandas and formatting

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 reduction etc. You need to remove the #! FIELDS part from the header. The modified header looks like time meanfree_sin_chi1_75 meanfree_sin_chi1_76 meanfree_sin_chi1_77 meanfree_sin_chi1_78Continue reading “Read COLVAR file using pandas and formatting”

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 had both upper and lower wall in my metadynamics simulation. Hence we have to correct the free energy surface for the walls andContinue reading “Reweighting Metadynamics”

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 codes on how to check convergence in metadynamics simulations. I ran two metadynamics simulations with DISTANCE CVs using Plumed 1.3 patched with GromacsContinue reading “Convergence of Metadynamics simulation”

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 details check here. It is a very recently developed technique which has a lot of promise. tICA can separate slow degrees of freedomContinue reading “tICA Metadynamics”

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 Zinc stays in co-ordination with two histidines (HID) and one glutamate as described in the following figure (Figure 1). Note: All the watersContinue reading “Parameter for zinc centre proteins”

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 State Models and also used as CVs to drive enhanced sampling simulations. Several dimensionality reduction techniques have been used over the years  suchContinue reading “Possible new idea with tSNE”

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 video on tSNE can be found here. The dataset used in this explanation can be accessed here (named combine_times_ca.dcd and corresponding GRO fileContinue reading “Analysis of MD trajectory using tSNE”

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 pip3 install –upgrade pip pip3 install jupyter Also you can install it with Anaconda. Details here  To run notebook  jupyter notebook This willContinue reading “Jupyter notebook and Matplotlib”

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 you want to dock all the ligands with receptors present in all the folders. You can use a script something like the followingContinue reading “Useful scripts”

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 especially with flaviviruses and the drug discovery targeting flavivirus proteases. That’s why ZIKA break into the scene of my research as ZIKA isContinue reading “Modelling of ZIKA proteases”