Gromacs analysis

[alevilla]

Hi
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RMSD shoots up

GROMACS version: 2020.2 GROMACS modification: Yes/No Here post your question Dear all, I am running a simulation of a complex molecule. it has two chain. When I calculated the rmsd and found that rmsd value shoots up at 16ns and 25ns. In corresponding PDBs two chains are far apart, out of the box. Is it artifacts? if the complex broke at 16ns why it re associates ? How can I fix it? Thank you [rmsd] [step16] [step25]

RMSD calculation

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 calcula…

Here you can find more on similar topic
https://gromacs.bioexcel.eu/search?q=RMSD%20jump

Best regards
Alessandra