How do I extract friction coefficient from the output files in GROMACS?

The thermal flux is computed as:

q=ξKbT1ndofS

where  ξ" id="MathJax-Element-2-Frame" role="presentation" tabindex="0">$\xi$ is the mean friction factor (which is obtained from the gromacs solver).

How do I extract friction coefficient from the output files in GROMACS?

### 1 Responses

1. Hello,

the friction factor can be extracted from the GROMACS trajectory using:

gmx energy -f your-file.edr -o your-friction-file.xvg -b (start time) -e (end time)

when you are asked to prompt, choose the group you want to extract the friction factor for, e.g.

vXi-NAMEOFTHEGROUP

Best wishes,

Luca Bergamasco & Matteo Fasano