[gmx-developers] thermal conductivity

[ta.matzerath at gmail.com]

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?

It would be awesome if i get an answer for my question,

Kind regards

Tanja

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