Re: [AMBER] translational diffusion coefficient from MSD

From: Daniel Roe <>
Date: Fri, 20 Jul 2018 11:01:20 -0400


On Sun, Jul 15, 2018 at 6:04 PM, Kris Feher <> wrote:
> It may very well be that longer simulation time would improve the values. What still does not fit is the fact that the MSD plots are not monotonously increasing. The displacement in whatever direction happens should increase the MSD value, don't you agree? I am particularly puzzled by the spike downwards at 50ns - as if the molecule would appear suddenly at the different place - I imagine a wrapping artefact would look like that....

I think you may be confusing displacement with cumulative distance.
Displacement at any time t is just the difference between position at
time t and position at time 0. Consider a hydrated cation that is
coordinating with e.g. DNA. It may move around a bit and "jiggle", but
while it's coordinated it won't move very far away from the DNA. Even
though the cumulative distance traveled over the course of the
simulation may be significant, in terms of diffusion it has stayed
right where it started.

Hope this helps,


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Received on Fri Jul 20 2018 - 08:30:02 PDT
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