Let’s get honest about sampling
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Molecular simulations see widespread and increasing use in computation and molecular design, especially within the area of molecular simulations applied to biomolecular binding and interactions, our focus here. However, force field accuracy remains a concern for many practitioners, and it is often not clear what level of accuracy is really needed for payoffs in a discovery setting. Here, I argue that despite limitations of today’s force fields, current simulation tools and force fields now provide the potential for real benefits in a variety of applications. However, these same tools also provide irreproducible results which are often poorly interpreted. Continued progress in the field requires more honesty in assessment and care in evaluation of simulation results, especially with respect to convergence.
KeywordsSampling Convergence Force fields and molecular simulations Binding affinity
DLM acknowledges the Louisiana Board of Regents Research Competitiveness and Research Enhancement Subprograms as well as the Louisiana Optical Network Initiative (supported by the Louisiana Board of Regents Post-Katrina Support Fund Initiative grant LEQSF(2007-12)- ENH-PKSFI-PRS-01), and the National Science Foundation under NSF EPSCoR Cooperative Agreement No. EPS-1003897 with additional support from the Louisiana Board of Regents.
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