[gmx-users] g_order (warning)

[Justin Lemkul]

On 1/15/14, 9:30 AM, shahab shariati wrote:
> Hi all
>
> I have DOPC lipid in my system. After preparing index file exactly based on
> how-to on the g_order page, I used following command to obtain order
> parameters of acyl chains:
>
> g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o
> order_sn1.xvg
>
> I encountered following warnings:
>
> WARNING: distance between atoms 779 and 781 > 0.3 nm (1.626940). Index file
> might be corrupt.
> WARNING: distance between atoms 995 and 997 > 0.3 nm (0.397073). Index file
> might be corrupt.
> WARNING: distance between atoms 1157 and 1159 > 0.3 nm (1.788146). Index
> file might be corrupt.
> WARNING: distance between atoms 1265 and 1267 > 0.3 nm (0.828453). Index
> file might be corrupt.
> WARNING: distance between atoms 76 and 78 > 0.3 nm (0.747680). Index file
> might be corrupt.
> WARNING: distance between atoms 346 and 348 > 0.3 nm (3.898362). Index file
> might be corrupt.
> .
> .
> .
>   After long time, deuter_sn1.xvg and order_sn1.xvg were obtained.
>
> How to remove these warnings? Are these warnings dangerous?
>

The warnings either indicate that the index groups were not constructed properly 
or that there is some wild behavior going on in the simulation.  The printed 
atom numbers correspond to carbons n-1 and n+1 in the calculation of the order 
parameters.  You can verify that the index groups are good by looking into the 
coordinate file to make sure they correspond to what you think they do.  To 
verify that the trajectory is sensible, you'll have to visualize it, focusing on 
the potentially problematic atoms that are printed out.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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