AI Article Synopsis
- Molecular dynamics (MD) simulations have significantly advanced since the 1950s, overcoming previous limitations related to size and duration due to improved algorithms and faster computing technology.
- With these advancements, MD can now explore longer biological timescales and a wider variety of conformational changes, including rare events.
- The study analyzes multiple simulations of the zinc finger NEMO protein (2JVX) of varying lengths (15, 30, 1000, and 3000 ns) to determine when shorter simulations are adequate versus when longer ones are necessary.
Article Abstract
Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600012 | PMC |
| http://dx.doi.org/10.1080/07391102.2015.1015168 | DOI Listing |
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