[gmx-users] Re: Error- Simulation box resizes during mdrun

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 12:26:24 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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