[gmx-users] g_order warning message

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 5 12:43:14 CEST 2009



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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

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

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



More information about the gromacs.org_gmx-users mailing list