[gmx-users] Is viscosity increasing in the system due to the protein unfolding?

[Dr. Vitaly Chaban]

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_750 at 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
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