[gmx-users] g_order warning message

[Justin A. Lemkul]

Andrei Neamtu wrote:
> Dear Justin,
> 
> thank you for your reply.
> 
> I am not trying to obtain the tethraedrality order parameter.
> I want to use the g_order on a linear flexible molecule grafted to the
> surface of the bilayer.
> I think that the usual united atom order parameter (the component on
> the direction perpendicular to the plane of the membrane) can give
> information about the degree of alignment of this grafted linear
> molecule (or an ensemble of molecules) with that axis. Do you think
> this is correct?
> 
> How exactly is the g_order parameter calculated in Gromacs? I couldn't
> find it in the manual.

The order parameter calculated by g_order is designed for use with lipids, such 
that deuteron positions are interpolated and the angle between the C-D bond 
vector and the normal is calculated.  The equation for the exact relationship 
between this angle and the order parameter appears in nearly every membrane MD 
paper.

Whether or not that is suitable for your purposes is up to you.  I doubt that it 
is, given the nature of your system.  If you really want to try, you'll have to 
probably override the 0.3-nm check in gmx_order.c and re-compile.  But in any 
case, g_order is going to try to reconstruct deuterons around whichever atoms 
you're analyzing.

-Justin

> 
> Andrei
> 
> On Wed, Aug 5, 2009 at 1:43 PM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
>>
>> Andrei Neamtu wrote:
>>> Hello,
>>>
>>> I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane.
>>> Because the distances between two atoms two bonds apart is greater
>>> than 0.3nm I keep receiving the message:
>>>
>>> .....................................
>>> Warming: distance between atoms ***** and XXXXX > 0.3 nm (******) .
>>> Index file might be corrupt
>>> Warming: distance between atoms ***** and XXXXX > 0.3 nm (******) .
>>> Index file might be corrupt
>>> Warming: distance between atoms ***** and XXXXX > 0.3 nm (******) .
>>> Index file might be corrupt
>>> Warming: distance between atoms ***** and XXXXX > 0.3 nm (******) .
>>> Index file might be corrupt
>>> Warming: distance between atoms ***** and XXXXX > 0.3 nm (******) .
>>> Index file might be corrupt
>>> ..................... and so on
>>>
>>> I think that writing out these messages reduces the performance of the
>>> g_order which takes a lot of time to complete.
>>>
>>> Does anyone know how to suppress these messages?
>>>
>> Not without changing the source code and re-compiling.  But is using g_order
>> on a CG membrane appropriate?  The bond between the coarse particles doesn't
>> even necessarily correspond to a C-C bond (or else you'd just be using a UA
>> force field), so I would think that the reconstruction of tetrahedrality is
>> not accurate.
>>
>> -Justin
>>
>>> Thank you,
>>> Andrei
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================