VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Mar 08 2016 - 09:59:30 CST

Hi Kevin,

It depends on what you mean by correctly... Without the -compound
fragment argument or something similar, the lipids molecules on the edge
of the box will be split across the periodic boundaries. Since your
protein is now in the middle, the lipids on the edge shouldn't matter if
the analysis script is written correctly to determine what is
"underneath" the protein. However as a practical consideration, I find
it easier to look at the trajectory without long bonds, so I usually add
in a -compound fragment argument to the pbc wrap command.

-Josh

On 3/8/16 3:20 AM, Kevin C Chan wrote:
> Dear Users,
>
> I have simulated a protein on top of a periodic multi-component
> membrane. During the simulation, the protein has moved to the edge of
> the unit cell and "flashing" between the edges due to PBC. I have
> tried PBCTools commands:
>
> pbc wrap -all -center com -centersel "selection of my protein"
>
> and it looks nice after wrapping. Here's the stupid question: are the
> lipids correctly wrapped so that I could correctly count number of a
> specific type of lipid underneath the protein?
>
> Thanks in advance.
>
> Regards,
> Kevin
>
> ​
> ​
> ----
> /PhD Candidate
> Department of Physics and Material Science
> City University of Hong Kong
> cchan2242-c_at_my.cityu.edu <mailto:cchan2242-c_at_my.cityu.edu>.hk/
>