[gmx-users] Identifying representative structures from a g_sham

Hi, Thanks for this - very helpful and I think I've been able to identify the structures I'm interested in. Incidentally, I saw the earlier correspondence about plotting the axes using g_sham. I'm having similar difficulties - I can generate axes, based on the data range using -xmax and -xmin

Re: [gmx-users] Identifying representative structures from a g_sham generated 2d energy plot

Hello, Since you already built 2-d free energy landscape (FEL), you should have PCs (PC1 and PC2) as a function of time. You also know from the minima of FEL at which PCs the system spends longer time. Once you find those PCs you should find when the system has those PCs (from PC vs time). Then you

[gmx-users] Identifying representative structures from a g_sham generated 2d energy plot

Hi, Having used g_sham to plot a Gibbs free energy landscape using a projection of the first two principal components from the normal covariance analysis (not dihedral PCA) like so: g_sham -f 2dproj_1_2.xvg -ls gibbs.xpm -notime I would like to now identify which parts of the trajectory are r