What is the good way to extract the representative PDB structure from 300 ns simulation

GROMACS version: 2021.1
GROMACS modification: Yes
I have obtained multiple 300-ns simulation and did some following analysis such as RMSF.
Now I want to extract the representative PDB structure from this 300-ns simulation.

I know we can use ‘gmx cluster’ (gmx cluster — GROMACS 2021 documentation) to do this.

Now the question is that: there are too many structures in the *.xtc file because I use the md.mdp configured with (dt = 0.002 ; 2 fs nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps). How can I use -tu and -b and -e options for just clustering those structures saying from 200ns - 300ns?

Or I must do clustering for the while 300-ns *.xtc file?

For the representative structure, be should it from the last saying 100-ns stable structure? must from the stable structures (checking by looking at the RMSD vs. time (ns), where supposing the last 100-ns give the stable line meaning no large fluctuates.)

Or can you give some suggestions how can I get the proper representative PDB structure for further analysis (e.g., comparing this wild-type structure with the structure from the mutation-based same 300-ns simulation)?



you can try gmx cluster -with the option -tu ns -b 200 -e 300

or in alternative you can use -dt option to reduce the number of frame to analyze

best regards

Hi Alessandra,

Thanks for your help. I will try that.