By default, H-bonds will be computed for all frames of a trajectory (can be restricted to just the current frame with the “coordsets false” option). You can also just compute the H-bonds between two residues, for example residues 13 and 17, and save the information (which will have all frames) to a file named “hbonds.txt” in your home directory with:

On Mar 28, 2025, at 8:07 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,
I am new in molecular simulation and not very much experienced with ChimeraX. Is there a way to keep track of H-bonds between two specific residues (they can form one or more H-bonds) during the course of the trajectories (in my case, .xtc files from gromacs)?
Thanks in advance
Sasha
________________________________________________________________________
Alexandra Zahradníková, PhD
Department of Cell Cardiology
Institute of Experimental Endocrinology
Biomedical Research Centre SAS
Dúbravská cesta 9
845 05 Bratislava
Slovakia
Mobile: +421 908 069 796

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