[gmx-users] how to calculate the viscosity of the bulk

Mon Feb 9 22:34:18 CET 2009

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 <gmx3 at 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: 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
>> > _______________________________________________
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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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-- 
Yanmei Song
Department of Chemical Engineering
ASU