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

Christopher Neale chris.neale at mail.utoronto.ca
Thu Oct 18 23:51:19 CEST 2012

We published the half-epsilon double-pairlist method for combining opls-aa/l proteins with Berger lipids in gromacs. An extension to amber protein and berger lipids was subsequently published by another group after our suggestions on this list. You can find my tips on how to extend the half-epsilon double-pairlist method to include amber proteins on this mailing list as we worked through the implementation for that other user and you can find a final write-up in their final manuscript.


-- original message --

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



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