First, it is unlikely that 'g_energy -f x.edr -o visc.xvg' provides you a viscosity.
Second, viscosity from equilibrium MD should converge vs. time before it can be analyzed. I guess what you observe is viscosity convergence, not viscosity evolution in response to unfolding. Dr. Vitaly V. Chaban On Tue, Apr 29, 2014 at 12:30 PM, fatemeh ramezani <fr_...@yahoo.com> wrote: > Dear Gromacs users > > I performed a simulation about the protein adsorption on the gold surface. > Protein fluctuation increased and it denatured after 10 ns simulation. By > calculating the viscosity of system by g_energy -f x.edr -o visc.xvg, I > founded that viscosity is increasing during the simulation. Due to the fact > that by unfolding of protein its viscosity increase, can I relate the > viscosity arising to the unfolding of protein? > > Fatemeh Ramezani > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
