RMSD calculation

User discussions
1

GROMACS version: 2020.4

Hi,

I am working with a complex includes protein, DNA and small molecule. After my 500 ns simulation, I used to want to calculate RMSD changes of this system during the simulation. I generated an index file with: gmx make_ndx -f complex.gro. And I gave an index to Protein+DNA+SmallMolecule. For RMSD calculation, I selected this group twice, however my RMSD values above 3.5 nm. If I choose Backbone or Protein groups twice, RMSD values are decrasing to ~0.2 nm.
I calculated each group seperately (Protein, DNA and Small Molecule) and the values are ~0.2 nm.
Is the problem about making index file or generating new group?

Thanks in advance

2

Probably you have pieces of your system jumping across periodic boundaries so the complex isn’t always together. Re-image with trjconv and you should be able to compute the RMSD of the whole complex.

3

Thank you for your answer.
However I applied image correction to my system and I am sure the system is not jumping. May my system has any other problem?

4

Without seeing your exact commands, selections, and the plots themselves, there’s not really much to go on.