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. The method was introduced in 2010 and generalized in 2011; its foundational papers are listed below.
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.
Please cite the following papers if you use this code.
Cite this publication
APA 7th edition
Patel, A. J., Varilly, P., Chandler, D., & Garde, S. (2011). Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling. Journal of Statistical Physics, 145(2), 265–275. https://doi.org/10.1007/s10955-011-0269-9
BibTeX
View BibTeXHide BibTeX
@article{quantifying-density-fluctuations-in-volumes-of-all-shapes-and-sizes-using-indirect,
note = {[Online; accessed 2022-06-21]},
author = {Patel, Amish J. and Varilly, Patrick and Chandler, David and Garde, Shekhar},
journal = {Journal of Statistical Physics},
doi = {10.1007/s10955-011-0269-9},
issn = {1572-9613},
number = {2},
year = {2011},
month = {10},
pages = {265--275},
title = {Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling},
url = {https://link.springer.com/article/10.1007%2Fs10955-011-0269-9},
howpublished = {https://link.springer.com/article/10.1007\%2Fs10955-011-0269-9},
volume = {145},
}
Cite this publication
APA 7th edition
Patel, A. J., Varilly, P., & Chandler, D. (2010). Fluctuations of water near extended hydrophobic and hydrophilic surfaces. The Journal of Physical Chemistry B, 114(4), 1632–1637. https://doi.org/10.1021/jp909048f
BibTeX
View BibTeXHide BibTeX
@article{fluctuations-of-water-near-extended-hydrophobic-and-hydrophilic-surfaces,
note = {[Online; accessed 2022-06-21]},
author = {Patel, Amish J. and Varilly, Patrick and Chandler, David},
journal = {The Journal of Physical Chemistry B},
doi = {10.1021/jp909048f},
issn = {1520-6106, 1520-5207},
number = {4},
year = {2010},
month = {2},
pages = {1632--1637},
title = {Fluctuations of water near extended hydrophobic and hydrophilic surfaces},
url = {https://pubs.acs.org/doi/abs/10.1021/jp909048f},
howpublished = {https://pubs.acs.org/doi/abs/10.1021/jp909048f},
volume = {114},
}
Installation and usage
The manual for the code includes instructions for its installation and use.
Support
Please post your questions, comments, concerns, and suggestions on the INDUS code’s Google Group.