VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Mar 08 2016 - 21:49:34 CST

Dear Josh,

Thanks for the reply. I will add the -compound fragment option for the sake
of "safety", though I did not see any splitting lipids for now. What I was
concerning is that as my protein moved to the edges in the original
trajectory, lipids on the opposite edge should also be considered as
"underneath the protein". Therefore, after wrapping, as my protein is now
wrapped to the middle of the box, could those lipids also be "correctly"
wrapped underneath the protein so that I could easily look at them using
representations such as within 10A of protein, etc.?

Thanks in advance for any experience shared.

Regards,
Kevin
​ 

----
*PhD CandidateDepartment of Physics and Material ScienceCity University of
Hong Kongcchan2242-c_at_my.cityu.edu <cchan2242-c_at_my.cityu.edu>.hk*
On Tue, Mar 8, 2016 at 11:59 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> 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 <cchan2242-c_at_my.cityu.edu>.hk*
>
>
>