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

Peter C. Lai pcl at uab.edu
Thu Oct 18 21:55:11 CEST 2012

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.

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