On 2/8/13 2:51 AM, Bharath K. Srikanth wrote:
Justin,
You're right, the density of the box does increase during the simulation.
How large is the increase in density?
But I don't believe the water is particularly sparse, since I've never
encountered this issue in previous simulations, when I used these
parameters for genbox while inserting water. The system density also
appears to have an acceptable value in the beginning.
Is there any other way I can approach this, for example, is there a
command/md.mdp option that would fix the size of my simulation box to the
initial values?
A fixed box is achieved by running in the NVT ensemble, but that may or may not
be appropriate for membranes.
-Justin
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 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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