[gmx-users] Re:Leaflet of Bilayer

minnale minnale_gnos at rediffmail.com
Mon Sep 22 15:05:39 CEST 2008

  Thanks alot to Chris and Alan for given their valuable suggestions

then a small doubt about time length of bilayer simulation, that is if I concentrate mainly on protein but not on membrane is it require to run >=50ns or 20ns of POPC alone before inserting protein into it.

 Earlier I performed only popc simulation for only 5ns then plotted potential energy(it came negative value), average area per lipid(0.64 nm^2/sec). Later protein embedded into 5ns simulated popc bilayer and being run simulations. 
What I have done was wrong? 
Appreciate for your help
Thanks in advance. 

>(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?

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