Re: [AMBER] diffusion path length

From: Daniel Roe <>
Date: Fri, 11 Jul 2014 13:57:34 -0600


On Fri, Jul 11, 2014 at 1:11 PM, newamber list <>

> I have some general query regarding diffusion. cpptraj diffusion command
> says
> 'In order to correctly calculate diffusion molecules should take
> continuous paths'

This just means that you should not have any imaging artifacts in your
trajectory (i.e. when your molecule "wraps" from one side of your cell to
the opposite side), otherwise you will artificially inflate the "velocity"
of that molecule for that frame.

> Ideally how long this path should be? infinite or some finite (if finite,
> then how much?). I am asking because somehow I am interested to know local
> diffusion in very small volume and as its a very small volume so one can
> not expect the same molecule to stay longer inside that volume and
> molecules will be exchanging quickly with molecules outside the considered
> box. Thus smaller will be the continuous path it will travel if moves out
> volume quickly.

If I understand what you are proposing to do, then it is currently very
difficult to do with cpptraj. You can calculate diffusion from the
mean-square displacement (MSD) using the Einstein relation:

2*n*D = lim(t->inf) MSD / t

The key is that this relation is valid as t approaches infinity, otherwise
your data will be too noisy; this is why the manual recommends averaging
over many atoms (in other words calculate diffusion for all waters, not
just one). What you would need to do is somehow filter out all waters
except those in the area of interest. You could *maybe* do this if the area
of interest is near some solute which can be used as a reference point,
then you use the "closest" command to retain a certain number of waters
near that area of solute. You would need to make sure you have enough atoms
and enough frames so that you are getting a good estimate of the diffusion
constant though; you would probably want to do something like see how your
answer changes vs the number of waters you add in etc.

Hope this helps,


> Any suggestions will be really helpful
> Thanks
> JIom
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jul 11 2014 - 13:00:02 PDT
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