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

klexa klexa at umich.edu
Thu Oct 18 21:04:34 CEST 2012

On 10/18/2012 11:53 AM, 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.

Okay, yes, it does seem much simpler. But if I can indeed just use a  
rectangular box like 7.7 7.7 10.5, why does Gromacs fail with the  
"triclinic too skewed" error?

{ -1.75e+25     0                   -0
-0                    -1.75e+25      -0
-0                      -0                -2.49e+25}

Maybe it's just related to this force field mixing, but otherwise, if  
I should be able to proceed with a rectangular box, does that need to  
be specified somewhere outside of when I use genbox to solvate my  
system with -box 7.7 7.7 10.5?

>> 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.

Great, I'm glad to hear it as I was skeptical too. I can tell you that  
after 2 months of trying to get a system like working, it still hasn't  
succeeded in any form, so the odds are not in its favor.
> -Justin
Thank you!

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