Extraction of minima structure from free energy landscape

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GROMACS version: 2023
GROMACS modification: No
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Hello everyone

I have used cover & anaeig module for PCA and sham module of gromacs for generation of free energy landscape (PCA and FEL) of my protein ligand complex…now I want to extract or visualize the conformations (minima or from other conformational space) and their timeframe…but the gibbs.xpm file doesn’t contain such information (only PC1 and PC2 coordinates and free energy value)…please help me in this regard. I mean how to dump the structure without knowing the timeframe?

2

hey,

You can use originlab software for 3d plot and get the global conformation coordinates and then using timestamp script dump the particular structure