[gmx-users] how to calculate the viscosity of the bulk
Berk Hess
gmx3 at hotmail.com
Tue Feb 3 09:58:43 CET 2009
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: jalemkul at vt.edu
> To: gmx-users at 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 at gromacs.org
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> >
>
> --
> ========================================
>
> 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
>
> ========================================
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