[gmx-users] viscosity calculation_2

[David van der Spoel]

On 2010-09-29 22.00, Payman Pirzadeh wrote:
> 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?
>
I think this is because it use an autocorrelation function of the 
pressure. By default it uses an FFT to compute it. The ACF at 20000 ps 
has very poor statistics (1 data point) and can therefore ruin the 
viscosity. Therefore ACFs by default are plotted to half the traj. There 
is a flag to get a longer (noisier) ACF. g_energy -h might tell you 
which one.

> 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