{"action":"opened","issue":{"url":"https://api.github.com/repos/MobleyLab/basic_simulation_training/issues/68","repository_url":"https://api.github.com/repos/MobleyLab/basic_simulation_training","labels_url":"https://api.github.com/repos/MobleyLab/basic_simulation_training/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/MobleyLab/basic_simulation_training/issues/68/comments","events_url":"https://api.github.com/repos/MobleyLab/basic_simulation_training/issues/68/events","html_url":"https://github.com/MobleyLab/basic_simulation_training/issues/68","id":346817394,"node_id":"MDU6SXNzdWUzNDY4MTczOTQ=","number":68,"title":"Revisions","user":{"login":"EfremBraun","id":6618019,"node_id":"MDQ6VXNlcjY2MTgwMTk=","avatar_url":"https://avatars1.githubusercontent.com/u/6618019?v=4","gravatar_id":"","url":"https://api.github.com/users/EfremBraun","html_url":"https://github.com/EfremBraun","followers_url":"https://api.github.com/users/EfremBraun/followers","following_url":"https://api.github.com/users/EfremBraun/following{/other_user}","gists_url":"https://api.github.com/users/EfremBraun/gists{/gist_id}","starred_url":"https://api.github.com/users/EfremBraun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EfremBraun/subscriptions","organizations_url":"https://api.github.com/users/EfremBraun/orgs","repos_url":"https://api.github.com/users/EfremBraun/repos","events_url":"https://api.github.com/users/EfremBraun/events{/privacy}","received_events_url":"https://api.github.com/users/EfremBraun/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-02T00:34:55Z","updated_at":"2018-08-02T00:34:55Z","closed_at":null,"author_association":"COLLABORATOR","body":"> A final essential topic is the difference between equilibrium and non-equilibrium systems.\r\nWe noted above that an MD trajectory is not likely to represent the equilibrium ensemble because the trajectory is probably too short.\r\nHowever, in a living cell where there is no shortage of time, biomolecules may exhibit non-equilibrium behavior for a quite different reason -- because they are \\emph{driven} by the continual addition and removal of (possibly energy-carrying) substrate and product molecules.\r\nIn this type of non-equilibrium situation, the distribution of configurations will not follow a Boltzmann factor distribution.\r\nSpecialized simulation approaches are available to study such systems~\\cite{Chong:2017:CurrentOpinioninStructuralBiology,  Zuckerman:2017:AnnuRevBiophys} but they are not beginner-friendly.\r\nNon-equilibrium molecular concepts pertinent to cell biology have been discussed at an introductory level (e.g. \\url{http://www.physicallensonthecell.org/}).\r\n\r\nWe haven't mentioned the different between equilibrium simulations and non-equilibrium simulations. Should we? If a beginner wants to simulate a Fickian diffusion coefficient, the impulse is to set up a non-equilibrium concentration gradient and measure the flux, when it's usually better to run an equilibrium simulation and get the diffusion coefficient from an autocorrelation function.\r\n\r\n> For example, the AMBER family force fields usually reduce 1-4 electrostatics to $\\frac{1}{1.2}$ of their original value,\r\n\r\nIs that right?"}}
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