[gmx-users] Leaflet of Bilayer

Alan Dodd anoddlad at yahoo.com
Mon Sep 22 10:05:52 CEST 2008

(Yes, what Chris Neale said).  I had to do something similar myself, to make a 256-lipid square box from a 128 lipid box.  I used genbox to make a new, larger square box using my original lipid patch as the input file, and then tinkered with the dimensions to get the lipids/leaflet as close to what I wanted as possible, then deleted the excess 1 or 2 lipids in one leaflet.  I wrote a small script to count the lipids in each leaflet, it's not hard to code and I found it immensely useful for generating leaflet-specific index files later.  I must admit, I only actually equilibrated it for 20ns or so.

----- Original Message ----
From: "chris.neale at utoronto.ca" <chris.neale at utoronto.ca>
To: gmx-users at gromacs.org
Sent: Monday, September 22, 2008 6:55:37 AM
Subject: [gmx-users] Leaflet of Bilayer

In my opinion, use any technique that you want (genbox included) then  
run the resulting system for >=50ns while plotting the area per lipid  
and order parameters over time. When these values stop drifting over  
time then you have an equilibrated bilayer. If you have access to a  
cluster that scales well to 4 cores then this should not take longer  
than a month. With systems that scale well to 10 cores I can  
equilibrate such a system in under two weeks. Of course, the more  
limited your resources are then the more thought that you need to put  
into your setup. Very generally, for beginners with at least moderate  
computational resources, I suggest immediately following your first  
good idea to get the system prepared and then, while it is running,  
starting to think about how it could have been done in a better way.  
With cpu resources as they are now, your initial run is likely to be  
finished faster than anything else if you start it immediately and the  
next time you go about this it will be faster because you will figure  
out the better method.

Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I  
as a reader am not going to have any problem with your final results  
even if I think that you could have obtained an equilibrated bilayer  
with a quicker method.

Important note: Please use a new subject for a new topic. I know that  
topics often diverge, but you started this thread with a vmd-list  
question and now you are on to something that is only related to that  
by the fact that you study membranes.


--- original message ---

Thanks for the response
Just diverting this topic to about specific number of popc molecules.

I created the bilayer by using genconf command
genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I  
posted  in my previous mail) generated output file contain 128 popc  
in each leaflet of bilayer.

If you see original popc box dimensions 6.1x6.2x6.9 (means in all  
dimensions popc number almost same)but with genconf command above  
mentioned options created box values 12x6.1x6.9. I dont want that many  
popc molecules because in X-dimension too many popc molecules are  

1.is there anyway to reduce those popc molecules from 128 to 80/90  
popc molecules? or
2.I wanted to create popc molecules 80 or 90 in eachleaflet is it  
possible to generate?

These are may be trivial queries
Could you give suggest me please
Thanks in advance.

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


More information about the gromacs.org_gmx-users mailing list