Dear all,
I have generated free energy landscape (FEL) plot by projecting Principal component 1 (PC1) and PC2 using g_sham program of GROMACS vs 4.6. But, I failed to understand how to extract the representative meta-stable conformations from FEL. From literature survey, I found the following figure attached below, where suitable conformations have been mapped across FEL. Please suggest me as how to generate such conformations in GROMACS?
Miłosz Wieczór
When you have your trajectory projected onto eigenvectors, just select the timeframes that correspond to the desired PC1 and PC2 values (inferred from the 2D plot) and dump the respective trajectory frames (e.g. using trjconv with the -dump option).
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