From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Fri Sep 30 2016 - 06:25:19 CDT
Nothing is wrong check out the Wrap commands.
On 09/30/2016 05:18 AM, faride badalkhani wrote:
> Dear NAMD experts,
>
> I have performed a simulation on a nanostructure in a water box and I
> did not get any errors. However, when I load the dcd file in VMD I see
> that almost half of the structure remains in the water box and the
> remain part of the molecule is out of the box. Could you tell me what
> is wrong with the simulation, please?
>
> regards,
> Farideh
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