Dr. Ramón Garduño-Juárez wrote:
Justin,
Regarding my question I forgot to tell you that after expanding the
system 4X, we have performed 26 shrinking steps at the 0.95 rate.
The system we are working with is one in which we have embedded two
proteins into the bilayer, one of them is a toxin and the other a
putative channel. Both proteins are docked in some way.
The last lines of the last shrinking step are:
-------
Area per protein: 10 nm^2
Area per lipid: 0.596104455536294 nm^2
Area per protein, upper half: 9 nm^2
Area per lipid, upper leaflet : 0.612233487794359 nm^2
Area per protein, lower half: 8.5 nm^2
Area per lipid, lower leaflet : 0.620298003923391 nm^2
Writing Area per lipid...
Done!
-----
The area per lipid of DMPC has been reported to be between 0.40 to 0.703
nm^2, with an average value of 0.656 nm^2
After visualizing of the system we found a that those lipid molecules at
the four corners of the box as disordered. That is, one of their tails,
or both, are far from the core of the bilayer. Nothing like the original
lipid box.
Do you think that we have shinked too much, or as you said, we have not
minimized long enough?
That's possible. InflateGRO tends to overestimate the true area per lipid, so
your DMPC may be compressed a bit more than you think. I usually stop DPPC
compression in the ballpark of 0.70 nm^2. If the lipids are reasonably close to
the rest of the system and not completely isolated in their own vacuum state,
then a gentle equilibration can bring everything together within a few ns.
-Justin
Cheers,
Ramon Garduno
El 09/02/2011 11:25 a.m., Justin A. Lemkul escribió:
Dr. Ramón Garduño-Juárez wrote:
Dear All,
First of all I want to tank Justin Lemkul and Thomas Piggot for their
useful comments that helped me to resolve my previous questions
regarding the construction of a lipid membrane.
Now I would like to post this question to this forum.
I got through placing a putative ion channel into a DPPC bilayer. I
managed to expand this sytem -> minimize it -> shrink it (several
times) -> minimize it (several times) until I got an adequate lipid
density.
After viewing the final results I noticed that there are several
lipid molecules that are dangling at the end of the periodic box.
Is this normal, or I did something wrong?. If this is expected, How
do I get rid of the dangling lipid molecules before I start a MD
simulation?
By "dangling" do you mean that they are somewhat isolated from the
rest of the lipids? If so, how many are there? Usually this just
indicates that you're not done shrinking the membrane back to
appropriate dimensions. The final box vectors achieved through
shrinking should usually be fairly close to the original dimensions of
the system. If this is not the case, then you're not done building
your system.
-Justin
Waiting for your replies...
Sincerely,
Ramon Garduno
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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