Hi James, > 1- I want to increase amplitude of the motions seen on the selected PCs but > I can't found scalling factor option for that.
The analysis gives you the amplitudes that are in your trajectory. Why do you want to amplify them to something probably non-physical? > > 2- I have calculated MD trajectory for my protein. From this trajectory I > want to find some relevant motions by means of PCA analysis. Also I have > dataset of the experimental structures of that protein where this motion > also presents ( e.g active and innactive conformations of my protein > included in my dataset) As the consequence I want to compare overal > direction of the motion observed along some PCs calculated from MD > trajectory ( it's called EDA) with the motion observed olong other PCs wich > was calculated from the enssemble of the pdb structures. As I've noticed > via g_anaeig I can compare such datasets by means of -v and -v2 flaggs. For > this purpose I must make trajectory for my X-ray structures at first and > load it with the MD trajectory into the g_anaeig -v md.trr -v2 x_ray.trr. > Would this aproach be correct in general ? What should I do if both of my > datasets consist of different number of backbone atoms (due to some missing > residues in the X-ray data) ? You have to make sure that the trajectories and the eigenvectors match. Then you have to think of what you want to do. - If you want to project the x-ray structures onto the eigenvectors from the MD simulations, you have to use g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb -proj - If you want to compare the similarity of the eigenvectors obtained from MD and from your crystal structures, you have to do PCA on both sets separately and then g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr -inpr Cheers, Tsjerk > > > Thanks for help, > > > James > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
