Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the ...

This repository contains Python code for running oxDNA umbrella sampling and large throughput simulations. This code is complementary to the article: Sample, Matthew, et al. "Hairygami: Analysis of ...

Comparison with unguided umbrella sampling reveals that the use of guided sampling encourages unfolding simulations to converge faster to a forced unfolding pathway that agrees with previous results ...

This script eases the setup up of Potential of Mean Force (PMF) windows in a reproducible manner. There are three main functions within the script: Initial setup of the umbrella windows Quality ...

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I will discuss an ensemble sampling scheme based on a decomposition of the target average of interest into subproblems that are each individually easier to solve and can be solved in parallel. The ...

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Praha 6, Czech Republic Article Views are the COUNTER-compliant sum of full text ...

Conformational Analysis Of Oligoarabinofuranosides: Overcoming Torsional Barriers With Umbrella Sampling. Journal of chemical theory and computation 2011, 7, 2989–3000.

Abstract: We propose an approach for addressing Reinforcement Learning (RL) problems. It combines the ideas of umbrella sampling, borrowed from Monte Carlo technique of computational physics and ...