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可 张

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">ξ is the mean friction factor (which is obtained from the gromacs solver).

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

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    Luca Bergamasco

    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

     

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