Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot.
2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: > Hello, > > I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity > of my system which is water. Two files are generate: *.xvg and the > enecorr.xvg. Now, what should I do to calculate the viscosity of my > system with these two files? Sorry for such naïve question. > Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin > > > Regards, > > > > Payman > > > > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 -- 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
