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

[Shanmuga]

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. 

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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