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I was looking for a dataset of alanine dipeptide trajectories. I was wondering whether there is such dataset available or it is unlikely to find one and I should start running molecular dynamics simulations myself. If so, what software would be easier to work with for a beginner.

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    $\begingroup$ Normally I'd do this with OpenMM or Amber using the Amber forcefield. However, I just learned about BALLView, ball-project.org/download, it seems to be a molecular viewer and modeler in one, which is convenient. Here is a tutorial, github.com/BALL-Project/ball/wiki/BV_MDSimulation. I could post this as an answer but I'm unfamiliar with the program. Just thought I'd share. $\endgroup$
    – Cody Aldaz
    Aug 21, 2020 at 23:08

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There are many sets, depending on force field or method (e.g., semiempirical, quantum, etc.) explicit or implicit solvent, etc., but if you're starting out, alanine dipeptide is one of the Amber tutorials, which include comparison production runs and analysis linked from the page:

http://ambermd.org/tutorials/basic/tutorial0/

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This link contains three independent simulations from the following papers:

  • F. Nüske, et al: Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias, J. Chem. Phys. 146 (2017), 094104.
  • C. Wehmeyer and F. Noé: Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics, J. Chem. Phys. 148 (2018), 241703.
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