Just to add to windy's results, this is a visualization artifact.
On Wed, Jun 17, 2015 at 1:40 PM, Morteza Chehel Amirani <
chehelam.ualberta.ca> wrote:
> Hello everyone
>
> I have performed a routine MD simulation in a water box with the periodic
> boundary conditions. When I load the output trajectory (with mdcrd format)
> in Chimera, it seems there is no box and water molecules spread in the
> space over the simulation time and the box is no more realized. I'm just
> wondering if anyone knows whether the problem is with the visualization of
> the results or something is wrong with the simulation parameters.
>
> Sincerely
> *Morteza Chehel Amirani*
> PhD Candidate
> Department of Mechanical Engineering
> University of Alberta
> 6-29 Mechanical Engineering Building
> Edmonton, Alberta, T6G 2G3
>
> http://www.ualberta.ca/~chehelam/
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 17 2015 - 21:30:03 PDT
