On 2/7/13 4:19 AM, Bharath K. Srikanth wrote:
Hi Justin:
Thanks for your reply. Yes, I did everything you mentioned. Let me explain
my steps in a bit more detail.
1) I had a lipid bilayer and a peptide from a previous simulation (in a
box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to the plane of the
bilayer). I removed the water and the peptides, so I had only the bilayer
left.
2) I then resized the box using editconf (the -box option) to a cubical
box of 7.5 nm in all directions. The bilayer remained in the center of the
new box.
But apparently you rotated the membrane, because (from the images linked below)
the plane is now in the x-z plane, which is very atypical and prevents you from
using semiisotropic coupling, which is normal for membrane simulations.
3) I then re-inserted the peptide by editing the coordinate file, and ran
an energy minimization. Then I added water using genbox, and ran another
EM.
4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
happening, I observed that the size of the box was beginning to change, in
the z direction (not in the y direction as I said yesterday, but still,
parallel to the plane of the bilayer).
I've included some pictures here (in the .tga format), from before and
after the simulation. When I ran it in vmd using the initial coordinates
and the trajectory file, I could actually see the box resizing during the
run.
https://www.dropbox.com/l/UJuFbDTPaISIpkSf
I'm sure there's a very simple explanation, but I can't seem to figure it
out.
It's hard to tell from the way things are rendered, but it seems to me that your
water is very diffuse, and over the course of the simulation, the density of the
system is increasing to try to fill a lot of void space. A simple analysis of
density should show this rather clearly.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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