Enhanced Sampling in Molecular Dynamics: Use of the Time

Aug 18, 2010 - In practice, however, the results of atomistic simulations are still affected by four ... representation of interatomic interactions(2-4, 9) (potential energy function with ..... (15) Note that truncated-polynomial local functions (of

Aug 18, 2010 - A new method, fragment-based local elevation umbrella sampling (FB-LEUS), ... searching and the umbrella sampling (US) conformational sampling approaches ... For a more comprehensive list of citations to this article, users are ... On

Feb 13, 2018 - ABSTRACT: We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originati

Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular ...

Feb 13, 2018 - They also conducted many short (0.5–1 ns) MD simulations and found a variety of trajectories that showed no significant bias in the unfolding velocity ..... Note that the computational efficiency of the ZMM was greater than that of t

Feb 13, 2018 - Using these results, we analyzed the conformational ensemble of the peptide via the free energy (potential of mean force) based on the radius of gyration (Rg), the principal component analyses (PCA) of the interatomic distances, and th

Feb 13, 2018 - The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically s

Oct 20, 2015 - Zheng , W.; Brooks , B. R.; Hummer , G. Protein Conformational Transitions Explored by Mixed Elastic Network Models Proteins: Struct., Funct., ...

Oct 20, 2015 - San Diego Supercomputer Center, 10100 Hopkins Drive, La Jolla, California 92093-0505, United States. ∥ Department of Chemistry and Biochemistry, ... in Crossref's Cited-by Linking service. For a more comprehensive list of citations t

Mar 21, 2011 - Enhancing QM/MM Molecular Dynamics Sampling in Explicit. Environments via an Orthogonal-Space-Random-Walk-Based Strategy.