Hi Carla, > during my simulation, the dimer I'm simulating changed a lot. > So when I calculate with g_rms, the RMSD between my initial and my final > structure (choosing "Protein-H"), I get a value of 10 angstroms.
Have you made sure there are no atoms jumping across the boundaries? > g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose > "chainA-H"), If you choose chainA-H, you'll get results for that chain. It will be used for the fit as well as for the analysis. > does g_rmsf fit one the whole dimer and then calculate rmsdeviation of > chainA or does it fit on chainA and then calculate RMSdeviation of chainA. > In the latter case, my result does not reflect the reality of my simulation. It does reflect the reality of your simulation. Maybe it does not reflect what you aimed to get. Cheers, Tsjerk -- 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 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