Tag: molecular dynamics
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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_78…
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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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Welcome to the homepage of Soumendranath Bhakat whose research interest is within the exciting field of biology, chemistry and computational applications. This webpage not only highlights current research interests, publications but also contains links of several softwares and servers used in the field of computational biology, molecular modelling and drug discovery. My current focus lies…
Life in Computational Biology 