Re: [AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj?

From: David A Case <>
Date: Fri, 30 Dec 2016 07:50:50 -0500

On Fri, Dec 30, 2016, wei wrote:

> I was calculating translational and rotational diffusion constants of
> a small sugar molecule. I haven't analyzed them before, so I need some
> suggestions.
> I wonder whether we should image atoms while performing translational
> and rotational diffusion constants analysis with cpptraj. In Amber16
> user manual, it is said that 'In order to correctly calculate diffusion
> molecules should take continuous paths, so imaging of atoms is
> automatically performed' in the section of 'diffusion' introduction. But
> if we wrap the atoms back into box, do we underestimate the movement of
> the molecule when the simulation time is sufficiently long?

Imaging, or lack thereof, would have no effect on rotational analysis.

Note that "imaging" and "wrapping" are not the same thing: if you are
interested in translation diffusion, you should probably not wrap your
simulation (i.e. set iwrap=0). But cpptraj will attempt to do the right
thing, even if you had set iwrap=1: it will image the molecules (if needed)
so that they exhibit continuous trajectories.

...hope this helps...dac

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Received on Fri Dec 30 2016 - 05:00:03 PST
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