AMBER Archive (2004)

Subject: Re: AMBER: RMSD calculations in ptraj and Carnal

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 15 2004 - 14:23:40 CDT

> whether RMSD means the same thing in ptraj and Carnal.

Carnal does mass-weighted RMS and ptraj didn't, but ptraj
may have this facility now, and anyway it shouldn't matter
if all the atoms being compared are carbons.

Are you fitting in all 3 cases? As a further test you could
produce a fitted trajectory by one method, and then measure
RMS by ptraj, carnal, and manually.

Bill
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