[gmx-users] viscosity calculation

[Warren Gallin]

265 K is -8C, so ice, not liquid water.

That would be more viscous than you might expect.

Waren Gallin

On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote:

> 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)?
> 
> Payman
> 
> -----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
> and 
> shear viscosity.
> 
> -Justin
> 
>> 
>> 
>> Regards,
>> 
>> 
>> 
>> Payman
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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