[gmx-users] g_order warning message

[Justin A. Lemkul]

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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-- 
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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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