dear gromacs users, i did PCA analysis for my trajectory using g_covar and g_anaeig, i have taken trajectory of 25ns from both protein alone and protein_withligands(i did two simulation one with ligands and other by removing the ligands from pdb file)and extracted eigenvalues along first 10 eigenvector, when i compared eigenvalues i find that protein_withligands has high values in compare to protein alone, but from literature protein alone is more flexible structure and after ligand binding it changes in to more rigid structure. primary analysis like RMSD, RMSF calculation showing high values for protein alone in compare to protien_withligands. i think i should also get higher eigenvalue for protein alone.. is any thing wrong with my trajectory. i had used same mdp file for both simulation. i am sending values of Ist 10 eigenvector for make my question more clear. any suggestion is appreciable protein-withligands 1 1.48497 2 0.674994 3 0.410547 4 0.279636 5 0.237182 6 0.213209 7 0.158359 8 0.140052 9 0.126227 10 0.113618
protein alone 1 0.526848 2 0.351471 3 0.267247 4 0.248945 5 0.222829 6 0.204475 7 0.158441 8 0.12583 9 0.0970591 10 0.0923962 thanks sanjay _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
