<P>
Thanks alot to Chris and Alan for given their valuable suggestions<BR>
<BR>
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.<BR>
<BR>
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. <BR>
What I have done was wrong? <BR>
Appreciate for your help<BR>
Thanks in advance. <BR>
<BR>
<BR>
>(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.<BR>
><BR>
><BR>
><BR>
>----- Original Message ----<BR>
> From: "chris.neale@utoronto.ca" <chris.neale@utoronto.ca><BR>
>To: gmx-users@gromacs.org<BR>
>Sent: Monday, September 22, 2008 6:55:37 AM<BR>
>Subject: [gmx-users] Leaflet of Bilayer<BR>
><BR>
>In my opinion, use any technique that you want (genbox included) then<BR>
>run the resulting system for >=50ns while plotting the area per lipid<BR>
>and order parameters over time. When these values stop drifting over<BR>
>time then you have an equilibrated bilayer. If you have access to a<BR>
>cluster that scales well to 4 cores then this should not take longer<BR>
>than a month. With systems that scale well to 10 cores I can<BR>
>equilibrate such a system in under two weeks. Of course, the more<BR>
>limited your resources are then the more thought that you need to put<BR>
>into your setup. Very generally, for beginners with at least moderate<BR>
>computational resources, I suggest immediately following your first<BR>
>good idea to get the system prepared and then, while it is running,<BR>
>starting to think about how it could have been done in a better way.<BR>
>With cpu resources as they are now, your initial run is likely to be<BR>
>finished faster than anything else if you start it immediately and the<BR>
>next time you go about this it will be faster because you will figure<BR>
>out the better method.<BR>
><BR>
>Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I<BR>
>as a reader am not going to have any problem with your final results<BR>
>even if I think that you could have obtained an equilibrated bilayer<BR>
>with a quicker method.<BR>
><BR>
>Important note: Please use a new subject for a new topic. I know that<BR>
>topics often diverge, but you started this thread with a vmd-list<BR>
>question and now you are on to something that is only related to that<BR>
>by the fact that you study membranes.<BR>
><BR>
>Chris.<BR>
><BR>
>--- original message ---<BR>
><BR>
>Thanks for the response<BR>
>Just diverting this topic to about specific number of popc molecules.<BR>
><BR>
>I created the bilayer by using genconf command<BR>
>genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I<BR>
>posted in my previous mail) generated output file contain 128 popc<BR>
>in each leaflet of bilayer.<BR>
><BR>
>If you see original popc box dimensions 6.1x6.2x6.9 (means in all<BR>
>dimensions popc number almost same)but with genconf command above<BR>
>mentioned options created box values 12x6.1x6.9. I dont want that many<BR>
>popc molecules because in X-dimension too many popc molecules are<BR>
>present.<BR>
><BR>
>1.is there anyway to reduce those popc molecules from 128 to 80/90<BR>
>popc molecules? or<BR>
>2.I wanted to create popc molecules 80 or 90 in eachleaflet is it<BR>
>possible to generate?<BR>
<BR>
>
</P>
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