Clustering analysis - Gromacs

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GROMACS version: 21.0
GROMACS modification: No
Can you please provide me a step by step command lines to complete clustering analysis and Free energy landsacape using modules : gmx cluster module & gmx sham module ?

2

Currently, a step-by-step guide is not available, but you can follow these steps:

Step 1: Prepare Your Trajectory: Make sure you have a GROMACS trajectory file (e.g., traj.xtc ,etc)
Step 2: Perform Clustering Analysis:
https://manual.gromacs.org/current/onlinehelp/gmx-cluster.html
e.g. gmx cluster -s conf.gro -f traj.xtc -o cluster.pdb -method linkage -cutoff 0.2 -clid cluster.log
Step 3: Generate Free Energy Landscape
https://manual.gromacs.org/current/onlinehelp/gmx-sham.html
Step 4: Visualize Free Energy Landscape
https://manual.gromacs.org/current/onlinehelp/gmx-xpm2ps.html

you can also use -h flag for more details in each step: gmx cluster -h

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