Dear Hicham Hboub

If for conformation you mean the peptide in a given 'shape', then you just have to look at your trajectory file and extract the frames which contain the geometry you are looking for.

Best

Nicola

Thank you for your reply dear Nicola Piasentin

I'm just wondering how could I extract the frames that contains the geometry ? Normally there's only one (.gro) file that contain shape of the final protein so do you know the exact command line to extract all of them ?

Dear Hicham Hboub

Take a look at gmx trjconv tool.

https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html

With something like

gmx trjconv -f your_trajectory.xtc -s your_tpr.tpr -sep snapshot_.gro

you will separate your trajectory in N snapshots, with N being the number of frames printed out during the run (which is decided when you set nestep and the nstxout-compressed in the .mdp file for the run).

This however will most likely print thousands of snapshots. You have to choose which conformations are interesting for you, understand at what time there is a conformer that respects such criteria, and then print out that conformation. If you print the position output quite frequently, the nearest (time-wise) geometries will be nearly identical.

Best

Nicola