Lesson plan

MDynaMix

Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90 (with Message Passing Interface (MPI) for parallel execution) . The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode. MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL).

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Article summary

Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90 (with Message Passing Interface (MPI) for parallel execution) . The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode. MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL).

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Discussion questions

  1. Summarise the article in your own words. Which single claim would you verify first, and why?
  2. Which claim in this article is most likely to be revised as the sources update? How would you check its current status?
  3. If two sources disagreed about one of these facts, what would you need in order to trust one over the other?

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