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
something
else. Kindly comment.
Thanks
*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
