Convergence of sampling in protein simulations Export

@article{citeulike:2308378, abstract = {With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations; but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling.}, author = {Hess, Berk}, citeulike-article-id = {2308378}, citeulike-linkout-0 = {http://dx.doi.org/10.1103/PhysRevE.65.031910}, citeulike-linkout-1 = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2002PhRvE..65c1910H}, citeulike-linkout-2 = {http://link.aps.org/abstract/PRE/v65/i3/e031910}, citeulike-linkout-3 = {http://link.aps.org/pdf/PRE/v65/i3/e031910}, day = {1}, doi = {10.1103/PhysRevE.65.031910}, journal = {Physical Review E}, keywords = {figata}, month = {March}, number = {3}, pages = {031910+}, posted-at = {2009-06-11 14:52:18}, priority = {2}, publisher = {American Physical Society}, title = {Convergence of sampling in protein simulations}, url = {http://dx.doi.org/10.1103/PhysRevE.65.031910}, volume = {65}, year = {2002} }

TY - JOUR ID - citeulike:2308378 L3 - citeulike-article-id:2308378 N2 - With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations; but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling. IS - 3 JF - Physical Review E TI - Convergence of sampling in protein simulations PB - American Physical Society VL - 65 SP - 031910 KW - figata AU - Hess, Berk PY - 2002/03/01/ UR - http://dx.doi.org/10.1103/PhysRevE.65.031910 ER -