Reading the index file wrong

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1

GROMACS version: 2020
GROMACS modification: No
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Hello users,

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:

For example:

sn1.index

[C1A]
8045 8057 8069 8081 8093 8105 8117 8129 8141 8153 8165 8177 8189 8201 8213…

**and **
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?

Thanks,
Soumya

2

Hi Soumya,

I suspect that your xtc does not contain the whole system and that is where the indices of the .tpr file and the xtc don’t match. gmx convert-tpr can give you a tpr file with only part of the system that would also match your xtc file - if I’m right and this is indeed the issue here.

3

I doubt gmx order will work for a CG system. It’s designed for united-atom, atomistic simulations. The large distance between particles is inherent to your system as coarse particles will be spaced differently than actual atoms.

Even if it did “work,” I wouldn’t trust the result, for the reason stated above.

4

Thanks @cblau
However, the xtc file contains the whole system here. Even if its not whole… atleast gmx would have read the atom number correct. That is where I am getting the error.

Thanks,
Soumya

5

Thanks @jalemkul

I actually saw some papers reporting the order parameters for CG systems. However, if gmx order is not designed for CG system, could you please suggest if there is any other alternative? or should I stick to the analysis at all atom level only?

Thanks,
Soumya