VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Mon Feb 05 2018 - 09:10:55 CST

If you feel like it you can give a try to my membrane builder included in
HTMD https://software.acellera.com/academic-download-htmd.html
It can create membranes of any dimensions and any composition you provide
it (given you have the topologies for the lipids. Currently it only
contains cholesterol popc and pope but it’s easy to extend).
It can also perform an equilibration if you want

from htmd.ui import *from htmd.membranebuilder.build_membrane import
buildMembrane
lipidratioupper = [['popc', 10], ['chl1', 1]]
lipidratiolower = [['popc', 8], ['chl1', 2]]
width = [50, 100]
bmol = buildMembrane(width, lipidratioupper, lipidratiolower,
equilibrate=False) # Writes by default the psfgen built system in
'./buildmemb/'
bmol.view()

​

On Mon, Feb 5, 2018 at 3:34 PM, thiagorrg UFC <thiagorrgarcia_at_alu.ufc.br>
wrote:

> Hello, VMD users
>
> I looked everywhere for this information but couldn't find it. I built a
> 90x90 membrane patch using membuilder.org, and I want to replicate this
> patch to form a larger membrane 180x180.
>
> I tried to use moveby on the original patch, saved it, but couldn't
> combine the different patches (because of same psf I think).
>
> What am I missing here? Does anyone have a suggestion?
>
> Thank you!
>