Free Software from the Zuckerman Group

Decorrelation Scripts: Click to Download

These scripts implement the analysis of simulation trajectories via the effective sample size, as described in http://arxiv.org/abs/q-bio.QM/0607037. The analysis operates on Tinker style trajectory archives, and calls the Tinker subroutine 'superpose' for calculating RMSD's. (go to http://dasher.wustl.edu/tinker/ to download Tinker, free of charge.) A detailed explanation of the usage and some idiosyncracies is found at the top of the file decorr-analysis.pl. Please email me with any questions or bug reports at , with the subject decorrelation time analysis.

Confidence intervals for hypergeometric variance: Click to Download

These scripts calculate confidence intervals on estimates of the variance of a hypergeometric distribution. This allows the addition of error bars to a theoretical prediction of such a variance, so that it may be ascertained whether an observation based on finite data falls within the expected fluctuation. (explanation PDF) Please email me with any questions or bug reports at , with the subject hyperG-CI.

Extrapolation Software: Click to Download

Nonequilibrium work values, generated for the purpose of obtaining free energy estimates with Jarzynski's relation, provide notoriously unreliable estimates. This results from the highly nonlinear nature of the exponential average, as discussed in several of our publications. Here you can download scripts to perfrom the analysis described in a recent paper [FM Ytreberg and DM Zuckerman, J. Comp. Chem., in press, (2004)]. The scripts will provide much more reliable free energy estimates than straightforward application of Jarzynksi's relation. They also provide auxiliary information, including finite-data block averages, to enable "manual" assessment of the estimates.