Hi, Berk: I saw your paper about the viscosity calculation method. Can you tell me what exactly I should do using GROMACS to get the fluid viscosity? I used GROMACS-3.3.3 single precision. Thanks a lot in advance.
On Tue, Feb 3, 2009 at 1:58 AM, Berk Hess <g...@hotmail.com> wrote: > Hi, > > This Einstein method of g_energy is extremely sensitive to the system setup. > You should have perfect pressure fluctuations, which probably means shifted > LJ potential, > PME, constant volume and double precision. > Some time ago I made a comparison of different methods: > http://dx.doi.org/10.1063/1.1421362 > Two of the methods can be used via the mdp option cos_acceleration and the > tool g_tcaf. > > David, I think we should remove the -vis option of g_energy, > since it will give nonsens, unless you know exactly what you are doing. > In that case you can also evaluate the Einstein formula "by hand" from the > pressure. > > Berk > >> Date: Mon, 2 Feb 2009 19:34:59 -0500 >> From: jalem...@vt.edu >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk >> >> >> >> Yanmei Song wrote: >> > Hi, Justin: >> > >> > I saw in the manual that by g_energy -vis the viscosity of the system >> > can be calculated. But when I perform the command i got this: >> > >> > @ title "Bulk Viscosity" >> > @ xaxis label "Time (ps)" >> > @ yaxis label "\8h\4 (cp)" >> > @TYPE xy >> > @ view 0.15, 0.15, 0.75, 0.85 >> > @ legend on >> > @ legend box on >> > @ legend loctype view >> > @ legend 0.78, 0.8 >> > @ legend length 2 >> > @ s0 legend "Shear" >> > @ s1 legend "Bulk" >> > 19.9601 182.954 131.299 >> > 39.9202 195.973 134.808 >> > 59.8802 209.345 130.015 >> > 79.8403 220.959 129.291 >> > 99.8004 227.397 133.514 >> > 119.76 224.858 128.183 >> > 139.721 234.26 124.201 >> > 159.681 239.432 112.779 >> > 179.641 233.247 90.5362 >> > 199.601 235.796 83.3315 >> > 219.561 232.205 80.3525 >> > 239.521 219.87 78.862 >> > 259.481 216.261 84.9063 >> > 279.441 221.782 81.2453 >> > 299.401 221.704 76.6335 >> > 319.361 212.225 83.4834 >> > 339.321 209.746 95.7125 >> > 359.281 208.776 100.049 >> > 379.242 209.623 101.467 >> > 399.202 204.93 111.357 >> > 419.162 196.223 117.499 >> > 439.122 198.347 121.818 >> > 459.082 200.15 118.537 >> > 479.042 203.718 105.464 >> > 499.002 209.584 98.6823 >> > 518.962 215.025 101.854 >> > 538.922 226.533 102.949 >> > 558.882 229.609 97.6396 >> > 578.842 228.081 96.0029 >> > 598.802 237.529 95.4091 >> > 618.762 245.169 95.4332 >> > 638.723 253.263 97.1168 >> > 658.683 251.794 86.5936 >> > 678.643 242.619 72.306 >> > 698.603 235.621 63.5751 >> > 718.563 230.813 67.5429 >> > 738.523 236.095 78.8719 >> > 758.483 240.001 84.0771 >> > 778.443 246.356 88.0818 >> > 798.403 256.28 91.1965 >> > 818.363 267.644 95.403 >> > 838.323 272.758 102.16 >> > 858.283 278.369 101.837 >> > 878.243 281.149 98.535 >> > 898.204 268.186 93.7993 >> > 918.164 254.442 81.3065 >> > 938.124 239.547 78.0454 >> > 958.084 221.896 87.4938 >> > 978.044 213.811 103.699 >> > 998.004 207.287 113.678 >> > >> > >> > My question is what the value should be for the viscosity of the >> > fluid. Should I average all the values of third column to get the >> > value. Does the value have a unit of cp? >> > >> >> Don't know, I've never done viscosity measurements before. Luckily, the >> Gromacs >> output is quite informative. Have you opened this file in xmgrace? It will >> make life a lot easier to read the graph. Units and legends are provided >> to >> indicate what the data mean. >> >> -Justin >> >> > Thank you so much in advance! >> > >> > Yanmei Song >> > Department of Chemical Engineering >> > ASU >> > _______________________________________________ >> > gmx-users mailing list gmx-users@gromacs.org >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> 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://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > ________________________________ > See all the ways you can stay connected to friends and family > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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? 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