[gmx-users] g_order (warning)

[shahab shariati]

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?

Any help will highly appreciated.