[gmx-users] viscosity using green kubo relation for ionic liquids

[David van der Spoel]

On 13/01/16 18:11, Shanmuga wrote:
> Hi all,
>
> I am comparing viscosity calculation with eq md and non eq md. I want to calculate viscosity in eq md with green kubo equation. Can anyone suggest me how to get stress tensor from pressure tensor and its auto correction plot.
>
Still gmx energy. Check all the options.
> Thanks in advance.
>
> Regards,
> Shanu
>
>> On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN <vvchaban at gmail.com> wrote:
>>
>> EqMD methods work poorly for highly and moderate viscous liquids.
>>
>>
>>
>>
>>
>>
>> On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram <shanmugam138 at gmail.com>
>> wrote:
>>
>>> I tried with g_energy -vis , but it calculates using einstein relation. I
>>> want to calculate using green kubo equation.
>>>
>>>
>>> regards,
>>>
>>> shanu
>>>
>>> On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
>>> spoel at xray.bmc.uu.se>
>>> wrote:
>>>
>>>>> On 11/01/16 22:54, shanmuga sundaram wrote:
>>>>>
>>>>> Hello all,
>>>>>
>>>>>
>>>>> I am trying to find viscosity using green kubo relation for Ionic
>>> Liquids.
>>>>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
>>>>> How
>>>>> to get stress autocorrelation function (SACF) from pressure
>>>>> autocorrelation
>>>>> function in MD simulations? Also how to change ACF windows (10, 50,
>>> 200ps)
>>>>> in getting autocorrelation function from gromacs (usually from g_analyze
>>>>> tool)?
>>>>>
>>>>> try
>>>> g_energy -vis
>>>>
>>>>
>>>>> regards,
>>>>>
>>>>> shanu
>>>>
>>>> --
>>>> 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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-- 
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