[gmx-users] viscosity calculation

[Payman Pirzadeh]

Apparently, in the file the unit in the file is cP. It might be the case
that I plotted the wrong column. I think I should get the third column.
Regarding the diffusion, I read in papers about rotational diffusion of the
proteins which could be calculated having the viscosity of the liquid and
hydrodynamic volume of the protein. So, volume could be calculated with
radius of gyration + 0.3nm of hydration shell and viscosity is given by
g_energy. So, a rotational diffusion constant could be theoretically
calculated.

Payman



-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: September 29, 2010 1:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation

On 2010-09-29 20.52, 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.
>
Is the experimental value 0.854 at that temperature?
Could be the the unit is different in the output too. Doesn't it say in 
the xvg file?

> 2. For calculation of protein diffusion constant, should we use the bulk
or
> shear viscosity of the solvent (water)?
Why not use g_msd?

>
> 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
>>
>>
>>
>>
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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