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-boun...@gromacs.org [mailto:gmx-users-boun...@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
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