[gmx-users] viscosity calculation_2

[Payman Pirzadeh]

Adding to my previous comments, It looks like that the third column is the
appropriate one to plot. However, I tried to use g_energy -b 0 -e 20000 to
take the whole trajectory (20000 ps) rather than half of the frames. But,
still g_energy take half of the frames. This has caused improper convergence
in viscosity values. If I take only the last 3000 ps (out of 10000ps), I
will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy
switches?

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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