Hi I have sort of a noob question about when to fit and when not to fit when computing rmsd and rmsf.
My use-case is to look at the motion of different domains of a protein where there are atoms near the COM of the starting structure that remain relatively stable throughout the simulation according to g_traj. Right now, I have been using trjconv -center the trajectory on this core alpha carbon then using trjconv -dump and grompp to generate a recentered starting structure .tpr. Then I am running g_rms or g_rmsf -nofit against the recentered .tpr as the reference. Is this wildly inappropriate? Should I be fitting against an index group consisting of that atom instead? Because the backbone is supposed to be shifting I want to minimize any artifacts that would potentially dampen an observable residue motion just because the rmsd was computed after a fit, and centering the trajectory on an atom near the starting COM would minimize distances traveled due to COM diffusion through the solvent. -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
