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.
Chris.
--- 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
present.
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@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
