[gmx-users] g_order warning message

[Andrei Neamtu]

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.

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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