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What are the units of force, velocity, and coordinates output by gromacs trajectory? In .mdp, they are specified by nstfout,nstvout,nstxout.

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nstxout, nstvout and nstfout are the number of steps between coordinates, speed and forces written in the output trajectory (Output control documentation).

As for the units present in your trajectory files (say a .trr): coordinates are in nm, speeds in nm.μs⁻¹ (so in mm.m⁻¹) and forces in kJ.mol⁻¹.nm⁻¹. These should be consistent through all GROMACS files (Definitions and Units documentation).

Note that .xtc files multiply coordinates by 1000 to compress them, so they are stored in pm (see GROMACS xtc documentation). Given MDAnalysis documentation on the subject, I believe .xtc files can only store coordinates, no speeds or forces.

I would be wary of softwares used to analyze your trajectory results (MDAnalysis, VMD, etc), as they may automatically do the conversion of these units, and for example show you coordinates in Å.

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  • $\begingroup$ This was a great answer O.Laprevote! We have a few unanswered GROMACS questions here, are you able to help us out at all with those? I'm trying to help take care of the unanswered queue. $\endgroup$ Jul 17, 2021 at 19:02

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