Hi,

With help of Plumed, I think it is doable.

In the CV section of the plumed documentation, you will find COORDINATION tool. It uses switching function to update the contact list between two groups within some cutoff.

You can utilise this tool during the MD run or after the run.

Before this you have to patch the plumed with gromacs.

To estimate protein-ligand contact frequency using GROMACS trajectory, you can follow these general steps:

You can use the following command:

gmx distance -f trajectory.xtc -s .tpr -n .ndx -select (LIG-Rec) -o .xvg

- This will help you to estimate the number of contacts between ligand and receptor. Then plot the .xvg file by excel or qtgrace or grace to see the frequency of the number of contacts.

If you want to select an atom of your receptor or specific atoms in your ligand you can use -seltype option. For your more information please see the following links:

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

or

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

The you may can calculate the frequency by contact_frequency = contact_frames / total_frames.

Alternatively, you may make index file as follow: gmx make_ndx -f .gro -o .ndx then use minimum distance command (gmx mindist) to calculate the number of close contants between your ligand and receptor in the .ndx file; gmx mindist -f trajectory.xtc -s .tpr -n .ndx -od mindist.xvg -pi -d 0.5

see the link below:

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