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

Peter C. Lai pcl at uab.edu
Thu Oct 18 23:41:49 CEST 2012

On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote:
> 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.

I was thinking along the lines of CHARMM for the bilayer and CGENFF for his
molecule (although rereading it sounds like he's just using standard
polypeptides, so yeah C36 for everything is probalby the way to go).

For Amber systems I thought people used a recent GAFF for the bilayer and 
Amber for the peptide. There was a 2010 or 2011 Plos paper on Beta2 
Adrenergic receptor that used a GAFF POPC bilayer and was run for 700ns.

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