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

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 21:58:22 CEST 2012

On 10/18/12 3:55 PM, Peter C. Lai wrote:
> On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
>> 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.
> Or just use a self-consistent FF and setup already published/validated for
> such a system, like AMBER+GAFF or CHARMM+CGENFF. The choice of forcefield
> combinations for a peptide-membrane system doesn't require completely
> reinventing the wheel these days.

One doesn't even need CGENFF for this; there are very good lipid parameters 
within the latest editions of the CHARMM force fields.  My suggestion was 
motivated by the mention of the Berger lipids that the OP was already trying to 
use.  Has anyone produced good lipid parameters using GAFF?  I recall seeing one 
or two papers a few years ago, but I think there was considerable refinement 
after the initial parameterization.



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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