Dear GROMACS users, I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in explicit water in the cubic box with 2fs time step.
I have used g_covar and g_anaeig to perform Principal Component Analysis/ Essential Dynamics analysis. But when I view the animation of the trajectory it, the movement of the protein looks weird. Can anyone please help to explain to me what I can do to get the right trajectory? Link for eigenvalue file: https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing I have used the following command line to extract the results: g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt mono_wild_filt1.pdb -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 pdb file link: https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 pdb file link: https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
