From: eprates_at_iqm.unicamp.br
Date: Mon Feb 09 2009 - 18:14:44 CST
Eric
In order to visualize the periodic cells in vmd you use the following patch:
1) load the trajectory in vmd
2) choose graphics menu item
3) select representations
4) select periodic
5) select the directions you want to check the neighboring cells.
About the way your are defining the PBC, it seems to be correct.
Erica
> 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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