Re: Basics of MD

From: Peter Freddolino (
Date: Tue Sep 08 2020 - 10:17:37 CDT

Dear Raman,
These are good questions, but they are also questions that are addressed in
any textbook or course on molecular simulation, and so I would highly
suggest that you seek out such information. Books like "Understanding
molecular simulation" (Frenkel/Smit) or "Molecular Modelling: Principles
and Applications" (Leach) are good starting points, as well as recordings
of one of the MMBioS computational biophysics workshops (which you can find
on youtube), are good starting points.

To give very brief answers to your two questions (which are absolutely not
a substitute for doing a lot of your own reading and study):

On Tue, Sep 8, 2020 at 7:02 AM Raman Preet Singh <> wrote:

> 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?\

ns are ns, to a reasonable approximation (there is certainly some fuzz, eg
many water models have different diffusive properties from real water, etc,
but these aren't order-of-magnitude differences). That means you have to be
either asking carefully posed questions that can be answered by looking at
ns timescale dynamics (or longer if you can run your simulations longer),
or you need to be doing clever things like enhanced sampling methods, free
energy calculations, etc. NAMD is good at integrating equations of motions
for a bunch of charged vdW spheres connected by specific bonded potentials.
Everything beyond that is up to you.

> 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?

It is almost always going to be best to run multiple replicate simulations,
each long enough to observe whatever phenomenon that you're interested in,
and ensure consistency between them or use them to figure out your
inferential uncertainty (just like you would not typically want to do an
experiment only once). In principle, if your system is at equilibrium and
you're interested in only equilibrium properties and you are sampling
sufficiently, the results of a single long simulation ought to be the same
as many shorter simulations, but that is a high-sampling limit that would
have to be validated.

> Thank you!
> Raman

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST