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Latest posts

  • 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 waters […]

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  • 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  such […]

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  • 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 file […]

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Learn to Explore

Great scientists, artists, entrepreneurs, sports persons are explorers. Following a path defined by the society and incentive structures kills the explorer mindset. Modern science need true explorers.

Make connections

Technologies are build by people. Bringing together a diverse set of people is necessary for substainable technological advancements. Make sure to build connections with people. It matters.

Biology is fascinating. Understanding biological functions at molecular level has significant implications in human disease. I help understanding molecular basis of biological events using physics-based simulations.