Welcome to the homepage for INDUS!

INDUS is an extension for PLUMED that implements the INDirect Umbrella Sampling method for biasing the coarse-grained number of particles, first introduced in this paper and generalized in this paper.

This page will be used to announce code updates and other important news regarding INDUS.

Getting the code

The INDUS code is open source and available on GitHub for anyone to use. We ask only that you give proper attribution and cite the relevant papers (listed below). This includes both using the code as-is and taking parts of it for use elsewhere.

View source on GitHub

  • Please cite the following papers if you use this code.
  • AJ Patel, P Varilly, D Chandler, and S Garde, "Quantifying Density Fluctuations in Volumes of All Shapes and Sizes using Indirect Umbrella Sampling", Journal of Statistical Physics, 145, 265 (2011). 

    @article{patel2011quantifying,
  title={Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling},
  author={Patel, Amish J and Varilly, Patrick and Chandler, David and Garde, Shekhar},
  journal={Journal of statistical physics},
  volume={145},
  number={2},
  pages={265--275},
  year={2011},
  publisher={Springer}
}
  • AJ Patel, P Varilly, and D Chandler, "Fluctuations of Water Near Extended Hydrophobic and Hydrophilic Surfaces", Journal of Physical Chemistry B 114, 1632 (2010). 

    @article{patel2010fluctuations,
  title={Fluctuations of water near extended hydrophobic and hydrophilic surfaces},
  author={Patel, Amish J and Varilly, Patrick and Chandler, David},
  journal={The Journal of Physical Chemistry B},
  volume={114},
  number={4},
  pages={1632--1637},
  year={2010},
  publisher={ACS Publications}
}

Installation and usage

The manual for the code includes instructions for its installation and use. It is available here .

FAQ

Please post your questions, comments, concerns, and suggestions on the INDUS code's Google Group .