[gmx-users] viscosity calculation using g_energy

[David van der Spoel]

Den 2018-04-08 kl. 17:31, skrev Ali Ahmed:
> Hello David,
> Thank you for your reply,
> After 5 ns of equilibrium, I run the simulation for 10 ns of heptane, but
> in the results of Einstein viscosity, I got only 5 ns.
> There are two files evisco.xvg and viscosity .xvg. In the first one, there
> are different columns but I think the last one is the viscosity of Einstein
> relation. The second one is the viscosity that I'm looking for.
> The results are far from the experimental results. Heptane experimental
> viscosity at 300 k is 0.376 cp but my results were so far as shown in the
> link below. Bulk viscosity goes to negative values which is incorrect.
> I'm confused a bit about the results and calculations.
> 
Please simulate ten times longer for largish compounds and use at least 
1000 molecules.

> https://ibb.co/cb5fjx
> 
> Thanks in advance
> 
> 
> On Sun, Apr 8, 2018 at 3:27 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
>> Den 2018-04-06 kl. 01:55, skrev Ali Ahmed:
>>
>>> Hello David,
>>> I have the same problem
>>> I run the simulation for 10 ns and I saved energies every 1 ps but the
>>> results were far and the curves go to negative values.
>>> Please, do have an idea how to get accurate results?
>>> Thank you
>>> Ali
>>>
>>
>> You give no information on numbers or what the einstein viscosity curve
>> look like.
>>
>>
>>
>>>
>>>
>>> On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <spoel at xray.bmc.uu.se
>>>>
>>> wrote:
>>>
>>> Den 2018-04-05 kl. 09:19, skrev Jo:
>>>>
>>>> Hello,
>>>>>
>>>>> I would like to calculate bulk and shear viscosity on gromacs using
>>>>> g_energy.  I have read a number of other emails about this topic but
>>>>> there
>>>>> still seems to be no conclusive answer to how to use this tool.  I use
>>>>> the
>>>>> following command:
>>>>>
>>>>> gmx energy -f  prod_500.edr -vis viscosity.xvg
>>>>>
>>>>>
>>>> The einstein viscosity is usually more accurate. How long is your
>>>> simulation and how often do you save the energies?
>>>>
>>>>
>>>>   From this, a file called 'viscosity.xvg' is produced with data on time
>>>>>
>>>>>>
>>>>>> (ps), shear viscosity, and bulk viscosity.  However, these values
>>>>> fluctuate
>>>>> wildly and are off from the correct viscosity for this model (SPCE) by
>>>>> at
>>>>> least an order of magnitude.  I know the simulation trajectory is
>>>>> correct
>>>>> as I have matched potential energy, density, and diffusion coefficition
>>>>> for
>>>>> these runs with literature.  However, the viscosity numbers are far off
>>>>> from the expected values.
>>>>>
>>>>> Any suggesions on what I can try?  I assume there must be a way to do it
>>>>> by
>>>>> hand via the pressure tensors.  Can someone directly me to how I can
>>>>> practically take the pressure tensors to calculate via Green-Kubo method
>>>>> the viscosity?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Shuwen
>>>>>
>>>>>
>>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>>
>>>> --
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>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se