[gmx-users] Box size/type confusion for bilayer system

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 20:53:38 CEST 2012

On 10/18/12 2:43 PM, klexa wrote:
> Hi Gromacs users,
> I think I am a bit confused about the proper way to handle boxes that are not
> standard cubes. I'm trying to run a membrane simulation where a cyclic
> undecapeptide is inserted into the membrane and I want the water layer to be
> sufficiently thick that if it were pulled, the peptide could be fully solvated
> by the water. To avoid having an enormous box of membrane and water, I have an
> orthorhombic box containing my peptide and bilayer. It minimizes alright with
> Gromacs, but when I go to equilibrate it it fails because it's too skewed to be
> a triclinic box. I've tried modifying the box with editconf and converting it to
> a rhombic dodecahedron, sort of like the manual suggests for a membrane system.
> I'm not sure that even that is sensible since it seems like I would be losing
> content that way, yet nothing is clipped, and I did this after using trjconv to
> remove any periodicity from my prior simulation of this system (in Desmond) but
> doing so gives me a starting potential energy of NaN for the new system that I
> obviously cannot work around. Is what I am trying to do even possible? If it is,
> it seems like there is probably a better way than the way I chose, so if you
> have any suggestions, I would be greatly appreciative.

I have never produced a membrane system with a hexagonal cross-section like the 
manual describes.  The most straightforward approach in my mind is simply a 
rectangular box.  It will save you a ton of headaches.

> I'm trying to run this simulation with AMBER FF99SB parameters for the peptide,
> Tieleman's lipid parameters for POPC, and SPCE waters, so just as a sanity
> check, is it reasonable to consider a system like that?

I don't know how this would even run.  The AMBER protein force field and Berger 
lipid paramters use different combination rules, and I have never seen a 
demonstration that one can use them together.  It is most straightforward to use 
a Gromos force field or OPLS-AA with modifications to account for the changes in 
combination rules.



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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