[gmx-users] Using SLLOD to find Viscosity

[nishi kashyap]

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 ?

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.
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-- 
Nishi Kashyap
Undergraduate
Chemical Engineering
IIT Delhi