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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