Re: [gmx-users] Reference structure for PCA.

Dear all! 1) I'd like also to know more about algorithm of the reference structure choosing. Commonly I'm using g_covar -f md.trr -s md.tpr fur PCA of the md trajectory ( here md.tpr is the protein topology and md.trr is the protein only trajectory) and g_covar -f ensemble.pdb -s ref.pdb for

Re: [gmx-users] Reference structure for PCA.

Hi Vivek, There are two distinct steps involved: (1) the fit of your trajectory to a reference structure, which corresponds to choose a conformation space; (2) the use of the PCA method, which corresponds to find in that space a new basis set whose ordered axes sequentially maximize dispersion

Re: [gmx-users] Reference structure for PCA.

Hi, The commands would certainly help, including the commands for getting the reference structure. Do note that the reference is the reference for fitting, which is 'external', i.e. provided by the user. This is not the same as the structure used to calculate the deviations, which is the average s

Re: [gmx-users] Reference structure for PCA.

Hi vivek, I have few questions related to your query: During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your co