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.

BEGR

This software is used to generate realistic structural ensembles for intrinsically disordered proteins. Please visit the official page http://begr.uidaho.edu/.

BERNOULLI'S PRINCIPLE DEMO

bernoulli-1.1.zip (updated Jul 2010)

This software was developed as an undergraduate student project to demonstrate Bernoulli's principle using kinetic theory and a Venturi nozzle.

If you use this software please cite:

Faulkner BE, Ytreberg FM,
Understanding Bernoulli's principle through kinetic theory simulation,
Am J Phys 79:214-216 (2011)
doi:10.1119/1.3533216

EXTRAPOLATION SOFTWARE

extrap-2.0.tgz (updated Oct 2008)This software extrapolates 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 25:1749-1759 (2004)
doi:10.1002/jcc.20103

INTERPOLATION SOFTWARE

interp-1.2.tgz (updated Oct 2008)

This software uses polynomial interpolation to fit thermodynamic integration free energy data. The tarball 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,
Accurate Estimation of Solvation Free Energy Using Polynomial
Fitting Techniques, J Comput Chem 32:134-141 (2011)
doi:10.1002/jcc.21609

REGRESSION SOFTWARE

regress-1.0.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 the bias and uncertainty of free energy estimates by using
polynomial regression to analyze thermodynamic integration data,
J Comput Chem 30:2297-2304 (2009)
doi:10.1002/jcc.21231