AMBER Archive (2004)

Subject: AMBER: diffusion coefficient with external applied electric field

From: Ioana Cozmuta (
Date: Tue Mar 02 2004 - 14:36:35 CST


I've run dynamics at 300K with the external applied electric field turned
on (the CM motion of the whole system is removed). Then I use ptraj to
calculate the diffusion coefficients and the following questions popped
up: there is a center of mass motion associated to each particle due to
the external applied electric field on top of the thermal motion. Would I
have to post-process the trajectory and remove for the selected particles
for which I am calculating the diffusion the "mean velocity" associated to
the presence of the electric field at each frame? Then calculate the
position of the particle again and from this the diffusion coefficient?

Any comments are greatly appreciated.

Thank you, Ioana
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