[gmx-users] Using SLLOD to find Viscosity

[David van der Spoel]

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