[gmx-users] viscosity calculation using g_energy

[Jo]

Hello,

I am trying to calculate the viscosity of pure SPCE water, which has a bulk
viscosity of 1.567 cP and shear viscosity of 0.704 cP according to
literature (https://pubs.acs.org/doi/pdf/10.1021/jp211952y).

In gromacs, I ran 1000 SPCE water using NPT equilibration for 20 ns and
then NVE production for 20 ns. I save to the energy file every 1 ps.  I
then run the following command to calculate viscosity:

gmx energy -f prod.edr -vis viscosity.xvg

I then enter the volume of the box from the final output gro file
(prod.gro), for 1000 SPCE water it is about 30nm^3.   I then observe the
resultant shear and bulk viscosity from the output viscosity.xvg file.

Both the shear and bulk viscosity vs time curves do not look converged and
appear to fluctuated over the range of 3-4 cP, with a mean of 1.4 cP for
shear viscosity and 2 cP for bulk viscosity.

Do you have any recommendations as to what I can try to reduce fluctuations
of viscosity to make an accurate prediction?





On Mon, Apr 9, 2018 at 4:39 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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
>>>>>
>>>>> --
>>>>> 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
>>> --
>>> 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
> --
> Gromacs Users mailing list
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