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
--
========================================
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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