[gmx-users] PCA and FEL

[sun]

Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis for the stability of my pro-lig complex.   In a 2015 paper, The group calculated two principal component, PC1 and PC2 and then prepared an.xvg file to be used as input for g_sham. My question is, when we use g_anaeig; we get eigenvec.xvg. from -comp flag. Now how shall one select two principal components from that data? I am sorry if my question is wrong but please help me. 

My second question is, can we use any two parameters like rmsd and Rg for input in g_sham to probe the stability of complex? Is that valid? 

With Regards
Suniba

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