# [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
> > _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> 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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