Re: Half of the structure goes out of the simulation box!

From: Ana Celia Vila Verde (
Date: Fri Sep 30 2016 - 07:31:03 CDT

Dear Faride,

When doing simulations in periodic boundary conditions, as you most
likely are, it is normal that a very large molecule appears to step out
of the main simulation box. The part of the molecule that appears out
of the box is in fact surrounded by water as well, and if you use a
surface representation for the water, you should see a hole in the water
on the other side of the box, indicating that the free part of the
protein is interacting with it. You can use the pbcwrap package in VMD
to refold your trajectory so that the big molecule is always at the
center of the main simulation box. Please do a search for this topic in
the NAMD list; you'll see many answers to it.



On 30/09/16 12:18, 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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