[gmx-users] Using SLLOD to find Viscosity

[nishi kashyap]

I have read both things thoroughly. I am new to this and so having a hard
time gathering basic concepts.
So, correct me if I am wrong:

To calculate shear viscosity in a PEG system:
1. Created a stable system and given cos_acceleration =0.05
2. Since I would know A(amplitude of acceleration),rho and k(wave index
number), I can find out the viscosity

Still, how do I find shear rate from that? Ideally, I should be changing
shear rate and finding viscosity. How can I do that ?

I might be asking very basic things but please help me here.


On Sat, Jun 3, 2017 at 3:25 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 02/06/17 22:12, nishi kashyap wrote:
>
>> Thanks for replying.
>> I have also tried that before. If we give the whole system the same
>> acceleration, then it wouldn't experience any shear. That was what I was
>> observing also.
>> Is there no way/ inbuilt method which use SLLOD , like in LAMMPS ?
>>
>
> Please read my email again carefully, and those references, in particular
> the Hess paper.
>
>
>
>> On Fri, Jun 2, 2017 at 4:09 PM, David van der Spoel <spoel at xray.bmc.uu.se
>> >
>> wrote:
>>
>> On 02/06/17 22:02, nishi kashyap wrote:
>>>
>>> Hi
>>>> I have a system of PEG for which I want to find viscosity. I want to use
>>>> SLLOD equations to find viscosity for a specific shear rate. I have read
>>>> allot about different ways , even tried to use 'deform'. But I did not
>>>> understand what do you mean by "off diagonal elements in a single
>>>> array".
>>>> I
>>>> am not able to understand. And also how do you intend to find shear rate
>>>> proceeding from that.
>>>> Could you please give some insight.
>>>> I would prefer if you just tell me how to use SLLOD equations? I really
>>>> need it, I have been trying this for so long.
>>>> Thank You
>>>>
>>>> Try using the cos_accel with a few different values.
>>>>
>>> See J. Chem. Phys. 119 pp. 7308-7317 (2003) and J. Chem. Phys. 116, 209
>>> 2002
>>>
>>> --
>>> 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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-- 
Nishi Kashyap
Undergraduate
Chemical Engineering
IIT Delhi