I am using Gromacs to analyze the interactions between protein-ligand.I am a beginner of Gromacs simulation. I have finished the simulation, I got the final gro , xtc, cpt, edr files, but not sure about how to do the data analysis. I read a research paper 'Characterization of the interaction of glycyrrhizin and glycyrrhetinicacid with bovine serum albumin by spectrophotometric-gradient flowinjection titration technique and molecular modeling simulations'. In this paper, they have done H-bond versus time graph and hydrophobic residue distance versus time graph, shown in attachment, to analyze the H-bond interactions and hydrophobic interactions between protein and ligand.
Does anyone know what command line can obtain these graphs and the steps?
Thanks a lot.
For hydrogen bond analysis gmx hbond tool from GROMACS may be helpful. For distance calculation you can use gmx distance tool. Please go through gromacs documentation before using these tools.
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Graphs