On Tue, Nov 24, 2015 at 8:45 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> The manual states that iwrap=1 "...can mess up...and other
> calculations." Can it be specified what these other calculations are?
>
​Diffusion and diffusion-related calculations. Anything that depends on
tracking a *particular* particle's trajectory​ through time will be messed
up by imaging/iwrap=1 (since the coordinates specified for a particular
atom may change from one image to another during the course of the
simulation).
However, assuming you have a continuous time series of trajectory files,
the "unwrap" command in cpptraj will reverse the effects of "iwrap=1" and
allow you to perform these kinds of calculations.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 24 2015 - 19:00:04 PST
