265 K is -8C, so ice, not liquid water. That would be more viscous than you might expect.
Waren Gallin On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote: > 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 > -- 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