RE: AMBER: Radius of Gyration and RMSD

From: Bill Ross <>
Date: Tue, 28 Oct 2003 09:21:10 -0800 (PST)

> 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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Oct 28 2003 - 17:53:01 PST
Custom Search