[gmx-users] Regarding cosine content

Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one

Re: [gmx-users] Regarding cosine content

Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one

Re: [gmx-users] Regarding cosine content

Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it mi

[gmx-users] Regarding cosine content

Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectivel