Hi Nithyanan, Right. So now we have that clear, I've had a look at the PDB file :p What you see is the result of filtering over a single eigenvector. You protein is kind of curling up through rotations of domains. You can't describe these rotations with a single eigenvector. They will be dispersed over multiple, and you will need at least two to capture the rotations. Maybe there's a twist associated and then you'd surely need one more.
As an aside, looking at the trajectory confirms me that this is a relaxation motion. I don't know whether you removed a ligand and this is a functional relaxation, or that is was started from a crystal structure, but it is something to be aware of. Hope it helps, Tsjerk On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai <nithyann...@gmail.com> wrote: > Hi Dr Tsjerk, > > I didn't do any clustering or make it whole. > > I just use the .xtc that I ontained after the simulation since I found out > there is no pbc effect of the protein. > > On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Nithyanan, > > > > How did you preprocess the trajectory? Did you cluster and/or make > > everything whole? > > > > By the way, 50 ns is probably too short for a protein of that size. It > will > > probably still be relaxing and the eigenvectors will be those of the > > relaxation. > > > > Cheers, > > > > Tsjerk > > > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai < > > nithyann...@gmail.com> > > wrote: > > > > > 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. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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. > > > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.