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

Bharath K. Srikanth s.bharath at iitg.ernet.in
Wed Feb 6 17:52:39 CET 2013

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

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.



Bharath K Srikanth
IV Year B.Tech
Dept. of Chemical Engineering
Indian Institute of Technology, Guwahati
Ph: (+91) 88762 03224
E.mail: s.bharath at iitg.ernet.in

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