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

[Shanmuga]

But in energy file we don't have stress tensor and some how we have to calculate stress tensor from pressure tensor. I am wondering how to get stress tensor from pressure tensor, in liquid md simulations. 

Regards, 
Shanu 

Sent from my iPhone

> On Jan 13, 2016, at 3:41 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 
>> 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
> -- 
> Gromacs Users mailing list
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