> 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Jun 15 2004 - 21:53:01 PDT
