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I did a liquid argon simulation at 100k. I forgot during analysis that I need to accommodate for the Periodic Boundary Conditions before doing any analysis which included distance. What are other such general things I should keep in mind during my analysis ?

I am rather novice to computational Science and might have missed even the most trivial things.

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I think that this question is too generic for a complete answer, as the latter would depend entirely on what you are simulating and what observables you are interested in. The only things that come to mind are

  • Remember to use relative velocities (relative to the system's centre of mass) when computing dynamical observables (such as the mean-squared displacement or the intermediate scattering function).
  • The radial distribution function makes sense only up to $r = L/2$, where $L$ is the side of the box.
  • If the system crystallises, be aware that you probably need NPT (that is, constant-pressure) simulations to get meaningful results.
  • Very close to a critical point (or to some other transitions/crossovers such as the percolation line) some quantities become heavily size-dependent, meaning that you need to do some extrapolations with the system size in order to get the "true" values.
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