VMD-L Mailing List

From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Fri Jan 04 2008 - 17:07:16 CST

Jnanojjal,

I have replicated lipid bilayers in the x and y direction several times.
Usually, I use the command $sel moveby "$xmove $ymove 0" to move the entire
system and then I write out several pdb files saving the new coordinates. I
then use grep, cat, and the redirect (>) commands to make a pdb file for
each segment (remember to watch the maximum number of residues per segment
when replicating large systems). Next, I use a script named reformat.sh to
renumber everything and then other scripts to create psf files and to merge
all of the segments into a single psf and pdb. I recently posted these
scripts to the Namd list here
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7069.html. Again,
there is most likely an easier way to do this, but this works for me.

Richard

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Chanda.Jnanojjal_at_edam.uhp-nancy.fr
Sent: Wednesday, December 26, 2007 3:08 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: replication of bilayer

Dear all

I have a very simple question. I want to replicate a lipid bilayer in x and
y
direction by using vmd. Is there any simple way to do it using VMD or any
text
commands?

bye

jnanojjal