Basics of MD

From: Raman Preet Singh (
Date: Tue Sep 08 2020 - 05:10:10 CDT

Dear All,

It's been a few months that I have been playing around with NAMD. During this time, there have been a couple of questions for which I couldn't find any convincing answers so thought of asking the experts in this group.

1. MD simulations are done on the scale of tens to hundreds of ns. Does this truly represent the timescales (ns) at which the observed phenomena occur in real-life situations (within a reasonable margin of error)? Has any validation been done in this regard? If the MD timescales do not really transform to real-life situations then what does ns really represent?

2. MD simulations are performed either as a single long simulation (upto several hundreds of ns) or multiple smaller simulations (tens of ns). Here, I would like to know what are the determinants for selecting a single long versus multiple small simulations. I would like to clarify here that by multiple small simulations I don't mean using restart files from a previous run and then continuing; rather, I mean multiple simulations all starting from the same initial configuration. Under what conditions should a single long versus multiple small simulations be used?

Thank you!


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