[AMBER] Is the RMSD using ptraj normalized with respect to residues ??

From: Himanshu Joshi <himanshuphy87.gmail.com>
Date: Thu, 9 Jan 2014 09:55:14 +0530

Hi folks,

I am using ptraj to calculate the RMSD of amber trajectories
with respect to initially minimized structure. Here is the command

rms reference mass out rms_trj time 1

I calculated RMSD for full structure (~ 50000 atoms) and it came ~ 1.1 nm,
while for few residues (350 atoms) of this structure RMSD is also near 1 nm,

Does the rmsd I got is normalized over no. of residues or I am missing
else. Kindly comment.


*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 5600*
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Received on Wed Jan 08 2014 - 20:30:02 PST
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