AMBER Archive (2003)

Subject: RE: AMBER: Radius of Gyration and RMSD

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> both ptraj and carnal can calculate RMSD w.r.t. a reference structure.

Note that carnal does a mass-weighted RMS and ptraj may only
treat all atoms the same (mass=1 as it were).

> I still cannot figure out how to calculate the radius of gyration
> (had the same question a few days ago).

In carnal, define a GROUP and then in OUTPUT TABLE specify groupid%radgyr

Bill Ross

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• Next message: Vikas Varshney: "AMBER: ibelly problem"
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• Maybe in reply to: Jagannadh B: "AMBER: Radius of Gyration and RMSD"
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