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

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 02:50:18 CET 2013

On 2/6/13 11:52 AM, Bharath K. Srikanth wrote:
> Hi everyone,
> Today, I was attempting a simulation of a system with a lipid bilayer, and
> the size of my simulation box, obtained from a previous simulation, was 15
> nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane
> of the bilayer). The bilayer consisted of 128 DOPC lipids and was located
> at the centre of the box. I used periodic boundary conditions in all three
> directions.
> I then resized the box to 7.5 nm in all directions, using the editconf
> -box option. After doing the requisite energy minimization steps, I ran
> the simulation using mdrun. However, running the simulation caused the box
> to gradually shrink in the y-direction (parallel to the plane of the
> bilayer!) during the simulation, ultimately settling at around half the
> original dimension. Is there anything I may have done that could cause
> this effect? I'm thoroughly baffled.

What do you mean by "resized the box?"  Did you strip out water, adjust box 
vectors, re-solvate, equilibrate, etc?  What you're describing is very weird; 
pictures, plots, etc would help a lot here.



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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