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Ytreberg group software
All software below can be freely used and modified. If you find a bug, please notify the developers at ytreberg -at- uidaho.edu.
EXTRAPOLATION SOFTWARE
extrap-0.3.tgz (updated Oct 2008)
This software attempts to extrapolate the work value data obtained from non-equilibrium Jarzynski-type simulations to obtain a more accurate value of the free energy difference.
If you use this software please cite: Ytreberg FM, Zuckerman DM, Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems, J Comput Chem 25:1749 (2004)
INTERPOLATION SOFTWARE
interp-0.3.tgz (updated Oct 2008)
This software uses polynomial interpolation to fit thermodynamic integration free energy data. The zipped file contained three directories, each with their own set of instructions for use. Our results suggest that use of interpolation reduces the bias and uncertainty of the free energy estimates compared to use of quadrature.
If you use this software please cite: Shyu C, Ytreberg FM, Use of polynomial interpolation to reduce bias and uncertainty of free energy estimates via thermodynamic integration, submitted http://arxiv.org/abs/0809.0882
REGRESSION SOFTWARE
regress-0.1.tgz (updated Oct 2008)
This software uses polynomial regression to fit thermodynamic integration free energy data. The zipped file contains a directory with a set of instructions for use. Our results suggest that use of regression reduces the bias and uncertainty of the free energy estimates compared to use of quadrature.
If you use this software please cite: Shyu C, Ytreberg FM, Reducing bias and uncertainty of free energy estimates by using polynomial regression to analyze thermodynamic integration data, J Comput Chem (2009), in press http://www3.interscience.wiley.com/journal/122240117/abstract
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