Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 20000 to take the whole trajectory (20000 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper convergence in viscosity values. If I take only the last 3000 ps (out of 10000ps), I will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy switches?
Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, 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. > Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? > 2. For calculation of protein diffusion constant, should we use the bulk or > shear viscosity of the solvent (water)? Why not use g_msd? > > 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 >> >> >> >> >> > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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
