Re: Periodic boundary condition in a membrane simulation

From: Nd S (navdeep79_at_gmail.com)
Date: Mon Feb 09 2009 - 18:05:20 CST

Eric,

To visualize periodic cells, on the TKCon Console (Extensions Menu) type

molinfo top set a length_in_x
molinfo top set a length_in_y
molinfo top set a length_in_z

in your case length_in_x = 102.7, length_in_y = 101, length_in_z = 83.5

Now got to Periodic Tab in the Representation window. Click +X, +Y +Z etc to
get more cells.

Navdeep

On Mon, Feb 9, 2009 at 5:28 PM, Eric Hu <eric.y.hu_at_gmail.com> wrote:

> Hi
>
> I am trying to run a md simulation with a protein embedded in water and
> membrane bilayer with namd2.6 in linux. I only add water in the z-axis to
> leave out the edges of the lipid bilayer so that the membrane extends in the
> x,y direction with other cells. The md.in of the periodic boundary
> condition (PBC) is set as the following:
>
> # Periodic Boundary Conditions
> cellBasisVector1 102.7 0 0
> cellBasisVector2 0 101.0 0
> cellBasisVector3 0 0 83.5
> cellOrigin 0.88 1.65 -1.86
> wrapAll on
> wrapNearest on
>
> After a short md run, the lipid molecules on the side start to flip
> randomly which is a sign of no contact with other lipid in the neighboring
> cells. I wonder if the way I set up the PBC is wrong. In addition, I wonder
> if there is a way to visualize the periodic cells (with VMD preferably)? Any
> suggestions will be appreciated. Thank you.
>
>
> Eric
>
>
>

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