Re: How to set setting periodic boundary condition

From: Chitrak Gupta (
Date: Fri Jul 07 2017 - 09:54:54 CDT

Hi Vidhya,

I have done something very similar. Unless your box size changes when you
merge the cyclic peptide, you should be able to use the previous cell basis
vectors. If you are generating your membrane using, they
provide equilibration scripts, and that generates *.xsc files which shall
have the box information. If not, I would say a good way to get an idea of
the box dimension is to do a measure minmax (VMD) on the waters. The idea
is that waters would give you a more accurate description of the box as
opposed to the lipids which would have tails sticking out of the box.

Hope this helps.

On Thu, Jul 6, 2017 at 8:43 AM, Vidhya Sankar <> wrote:

> Dear Namd user
> I want to set Periodic Boundary condition
> for My Protein/Lipid membrane . My system contain Assembly of cyclic
> peptide placed 2 Armstrong Distance above the Z axis of Lipid Membrane
> Lipid Membrane . How to set Cell basis vector ? May i follow the Membrane
> tutorial as usual.
> I need your valuable suggestion

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