GROMACS version: 2020
GROMACS modification: No
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I want to calculate the order parameter of my lipid molecules. I made a index file using make_ndx. I generated sn1.ndx and sn2.ndx. When I run the gmx order command and supply the index files (sn1 or sn2) giving the same *.tpr that was used to generate the index file, every time it is reading the wrong atom number as the starting residue:
8045 8057 8069 8081 8093 8105 8117 8129 8141 8153 8165 8177 8189 8201 8213…
in the run log file:
Groupname: C1A First atomname: C1A First atomnr 8044.
and then it gives warning like
"WARNING: distance between atoms 8044 and 8046 > 0.3 nm (0.857496). Index file might be corrupt."
I have tried changing the selected atom also every time it reads a number less than the original.
This is a Coarse Grained system, I have tried generating order parameter for all atom system and it works fine.
This is the command I have used:
gmx order -f traj.xtc -s md_production.tpr -od deuter_sn2.xvg -n sn1.ndx
Its really difficult to figure out the error. How do I proceed with the calculations?