[gmx-users] viscosity calculation

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Sep 29 20:52:12 CEST 2010

Well, two questions:

1. My bulk values are fluctuating around 60 (I assume cP). But it looks like
very weird to me since experimental value for water viscosity is 0.854 cP.
My system is at 265K with 4202 molecules. Is sth strange going on? Or I am
missing some unit conversions in the plot.

2. For calculation of protein diffusion constant, should we use the bulk or
shear viscosity of the solvent (water)?


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: September 29, 2010 12:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation

Payman Pirzadeh wrote:
> Hello,
> I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity 
> of my system which is water. Two files are generate: *.xvg and the 
> enecorr.xvg. Now, what should I do to calculate the viscosity of my 
> system with these two files? Sorry for such naïve question.

Plot the output .xvg; you will find it should contain two quantities: bulk
shear viscosity.


> Regards,
> Payman


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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