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

[Justin A. Lemkul]

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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