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Hi,<br><br>This Einstein method of g_energy is extremely sensitive to the system setup.<br>You should have perfect pressure fluctuations, which probably means shifted LJ potential,<br>PME, constant volume and double precision.<br>Some time ago I made a comparison of different methods:<br>http://dx.doi.org/10.1063/1.1421362<br>Two of the methods can be used via the mdp option cos_acceleration and the tool g_tcaf.<br><br>David, I think we should remove the -vis option of g_energy,<br>since it will give nonsens, unless you know exactly what you are doing.<br>In that case you can also evaluate the Einstein formula "by hand" from the pressure.<br><br>Berk<br><br>> Date: Mon, 2 Feb 2009 19:34:59 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] how to calculate the viscosity of the bulk<br>> <br>> <br>> <br>> Yanmei Song wrote:<br>> > Hi, Justin:<br>> > <br>> > I saw in the manual that by g_energy -vis the viscosity of the system<br>> > can be calculated. But when I perform the command i got this:<br>> > <br>> > @ title "Bulk Viscosity"<br>> > @ xaxis label "Time (ps)"<br>> > @ yaxis label "\8h\4 (cp)"<br>> > @TYPE xy<br>> > @ view 0.15, 0.15, 0.75, 0.85<br>> > @ legend on<br>> > @ legend box on<br>> > @ legend loctype view<br>> > @ legend 0.78, 0.8<br>> > @ legend length 2<br>> > @ s0 legend "Shear"<br>> > @ s1 legend "Bulk"<br>> > 19.9601 182.954 131.299<br>> > 39.9202 195.973 134.808<br>> > 59.8802 209.345 130.015<br>> > 79.8403 220.959 129.291<br>> > 99.8004 227.397 133.514<br>> > 119.76 224.858 128.183<br>> > 139.721 234.26 124.201<br>> > 159.681 239.432 112.779<br>> > 179.641 233.247 90.5362<br>> > 199.601 235.796 83.3315<br>> > 219.561 232.205 80.3525<br>> > 239.521 219.87 78.862<br>> > 259.481 216.261 84.9063<br>> > 279.441 221.782 81.2453<br>> > 299.401 221.704 76.6335<br>> > 319.361 212.225 83.4834<br>> > 339.321 209.746 95.7125<br>> > 359.281 208.776 100.049<br>> > 379.242 209.623 101.467<br>> > 399.202 204.93 111.357<br>> > 419.162 196.223 117.499<br>> > 439.122 198.347 121.818<br>> > 459.082 200.15 118.537<br>> > 479.042 203.718 105.464<br>> > 499.002 209.584 98.6823<br>> > 518.962 215.025 101.854<br>> > 538.922 226.533 102.949<br>> > 558.882 229.609 97.6396<br>> > 578.842 228.081 96.0029<br>> > 598.802 237.529 95.4091<br>> > 618.762 245.169 95.4332<br>> > 638.723 253.263 97.1168<br>> > 658.683 251.794 86.5936<br>> > 678.643 242.619 72.306<br>> > 698.603 235.621 63.5751<br>> > 718.563 230.813 67.5429<br>> > 738.523 236.095 78.8719<br>> > 758.483 240.001 84.0771<br>> > 778.443 246.356 88.0818<br>> > 798.403 256.28 91.1965<br>> > 818.363 267.644 95.403<br>> > 838.323 272.758 102.16<br>> > 858.283 278.369 101.837<br>> > 878.243 281.149 98.535<br>> > 898.204 268.186 93.7993<br>> > 918.164 254.442 81.3065<br>> > 938.124 239.547 78.0454<br>> > 958.084 221.896 87.4938<br>> > 978.044 213.811 103.699<br>> > 998.004 207.287 113.678<br>> > <br>> > <br>> > My question is what the value should be for the viscosity of the<br>> > fluid. Should I average all the values of third column to get the<br>> > value. Does the value have a unit of cp?<br>> > <br>> <br>> Don't know, I've never done viscosity measurements before. Luckily, the Gromacs <br>> output is quite informative. Have you opened this file in xmgrace? It will <br>> make life a lot easier to read the graph. Units and legends are provided to <br>> indicate what the data mean.<br>> <br>> -Justin<br>> <br>> > Thank you so much in advance!<br>> > <br>> > Yanmei Song<br>> > Department of Chemical Engineering<br>> > ASU<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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