Tag: python

  • 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 […]

    Continue reading

  • 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 will […]

    Continue reading