[gmx-users] g_order

[shahab shariati]

Dear gromacs users

To resolve my previous issue, I used info in the how-to on the g_order page
and I checked index file and made a new index file. This time, when I use
g_order -s md.tpr -f md.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o
order.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.xvg were obtained. This time,
these files are not empty.

I have 2 questions:

1)  How to remove these warnings? Are these warnings dangerous?

2) What is difference between "Scd" and "S" parameters in deuter_sn1.xvg
and order.xvg files?


Best wishes