Hi Bob, >From reading the source code gmx_anaeig.c it seems that the fitting is only performed when a fit-structure is present in the eigenvector file. That means that -proj should give what you want as it is. The help seems to incorrectly state that the reference is used for fitting if a fit-structure is not present in the eigenvector file. Probably one of the developers should have a look at this.
Best, Tsjerk On 9/27/07, Robert Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > I'm performing PCA on single stranded DNA adsorbed to a carbon > nanotube which is aligned along the z-axis. Because the DNA is > adsorbed, fitting each frame to the average structure via a 3D > translation and rotation doesn't make sense. In my analysis, I > minimize the RMSD between each frame and the average DNA structure by > the following algorithm: > > 1. Translate instantaneous DNA structure along the z-axis such that it > has the same center of mass z-component as the average structure (i.e. > z_com = z_com_avg) > > 2. Apply a rotation about the nanotube axis to minimize the RMSD > between the instantaneous and average structures. > > I perform this fitting on each frame of my trajectory using scripts > that I wrote for VMD and save the resulting RMSD-minimized trajectory. > I then construct and diagonalize the covariance matrix using the > following command: > > g_covar -s average.pdb -f fit-trajectory.xtc -nofit -noref > > Here, average.pdb is the average DNA coordinates. Since I have already > manually fitted my trajectory, I use the -nofit and -noref flags. > > Now, I would like to project my fitted trajectory along the > eigenvectors obtained from g_covar. However, it seems that g_anaeig > will automatically fit your trajectory to the first frame in > eigenvec.trr. Since I have already manually fitted my trajectory, I > want to skip this additional fitting step. However, it doesn't seem > like there is a way to do this. Does anyone have any suggestions about > how I could proceed? > Thanks, > Bob > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
