VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Oct 07 2016 - 05:52:26 CDT

Hi Roshan,

Right after you build the structure, measure minmax $all (like Ajasja
mentioned) is a good measure. However, once you start running the
simulation, the lipid chains are going to stick out of the periodic box,
which means the above command will give you huge overestimstes of the
dimension.

At that time, you could use the *.xst file for the x and y (and z as well)
dimensions of the system.

Hope this helps,
Chitrak.

On Oct 7, 2016 6:48 AM, "Ajasja Ljubetič" <ajasja.ljubetic_at_gmail.com> wrote:

Sure there is, just load it in VMD and use measure minmax
<https://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node136.html>.
Best,
Ajasja

On 7 October 2016 at 11:27, Roshan Shrestha <roshanpra_at_gmail.com> wrote:

> I have created a POPC membrane using CHARMM builder, but I am not sure
> about its dimension though. Is there any way to know or look at its
> dimensions. Thanks
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
>
>
>