[gmx-users] Using SLLOD to find Viscosity

[David van der Spoel]

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