Hi Shahab, > I want to know exactly how do radius of gyration of protein from free state > to complex state change . > Rg increased od decreased?
That depends on the protein. Some will, e.g., close or fold upon binding, while others may open up, or unfold. > I want to know my data [ In my simulation systems, the average of radius of > gyration in free protein > is 2.31 and for protein in complex is 2.58.] is true? It's true, because you found it. Whether it correctly reflects the state of the system you're after depends on the quality of your model, the time scale simulated and the tims scale of conformational changes involved in (un)binding. There's no rule of thumb. 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
