From: Jerome Henin (
Date: Sat Oct 07 2006 - 11:33:03 CDT

A reminder for all users of this list:
It is considered bad practice to attach large files to mailing list messages.
Bulky data should be made available by other means, only to those concerned.

The only way I see would be to generate a list of lipids to be deleted using a
VMD script (using atomselect with a selection text with criteria on the x and
y positions). Then these lipids can be deleted from a PDB file using another
script in whatever language you like (awk is pretty efficient for that if you
use a unix-like OS) or by hand if it is faster for you than coding. The
resulting bilayer would require a very careful equilibration so that the gaps
get filled with lipids, not water.

> Dear VMD users
> I have a hydrated lipid bilayer of 288 DMPC molecules.
> This lipid bilayer is a little big for what i require for
> embedding my GPCR protein (280 aa). I have realized that for
> my system 80A x 80A POPC bilayer generated works fine
> keeping enough gaps on all xyz directions.
> However, I want to use this pre-equilibrated DMPC 288
> bilayer.
> Now can anybody tell me a way in VMD by which I can cut
> short this bilayer to roughly 80A x 80A in X/Y directions. I
> want to cur this bilayer in X/Y dimensions to get to
> appropraite size so that i don't waste computational time
> more than what is absolutely necessary.
> What commands in VMD can solve this purpose? I will eagerly
> wait for suggestions to do the same.
> Kind Regards
> Akshay Patny (Olemiss)