VMD-L Mailing List

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Thu Oct 05 2006 - 21:23:43 CDT

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)