[gmx-developers] thermal conductivity

[David van der Spoel]

On 07/05/17 23:05, ta.matzerath at gmail.com wrote:
> Hey,
>
>
>
> i am new in Gromacs and i am trying to get the thermal conductivity for
> the Alkane series. I want to try the green-kubo formula, but i noticed
> soon, that there is no tool in gromacs to get the heat current vector
> aurocorrelation. So i thought i just can get the different components
> like the velocities, the total energy, the interaction force between two
> molecules and the distance between two molecules. Then i would put those
> files into a script to calculate the thermal conductivity.
>
>
>
> But i don´t know how to get the interaction Force between two molecules.
> Gromacs always Shows me the Force which one molecule experienced over
> the Simulation. for example if i put N=1000 ethane molecules in a box
> for Simulation, i Need (N*(N-1))/2 forces Fij between molcule_i and
> molecule_j over the time.
>
>
>
> Is there any solution to fix my Problem?
Not really, these forces are not even stored internally. In addition use 
of long-range periodic forces through Ewald summation makes this 
ill-defined. You may want to look into other algorithms, although I am 
not aware of one.
>
>
>
> It would be awesome if i get an answer for my question,
>
>
>
> Kind regards
>
>
>
> Tanja
>
>
>
> Gesendet von Mail <https://go.microsoft.com/fwlink/?LinkId=550986> für
> Windows 10
>
>
>
>
>


-- 
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