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The Living Journal of Computational Molecular Sciences is a journal for manuscripts which share best practices in molecular modeling and simulation. These works are living documents, regularly updated on GitHub with community input, and can include perpetually updated reviews, tutorials, comparisons between software packages, and other documents which aim to improve the studies in the field. The best practices and tutorials papers are of particular use!
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The Open Force Field Initiative includes many resources for easily parameterizing a wide range of molecular systems, including tutorials.
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AmberTools is a software suite for creating Amber topologies, including the popular tleap approach.
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i-CoMSE has run a online workshop introducing enhanced sampling techniques, ways to increase the rate that molecular simulations visit the high-probability configurational esembles that are kinetically separated, and the videos, slides, and code for these are available at the link above. In particular, this page gives even more ideas and resources for enhanced sampling simulations.
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Bootstrapping is a robust technique for estimating uncertainties in calculations without assuming that the distributions are Gaussian or doing messy calculus. We didn't quite get to it this time, but have an earlier i-CoMSE tutorial on this technique.
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Signac is a tool for managing large numbers of simulations. The notebook shown during the workshop to demonstrate running Signac is posted here.