[gmx-users] doubt in RMSD

[Seera Suryanarayana]

Dear gromacs users,

I have done simulations for 100ns. My peptide length is 25 residue length.
While calculating the RMSD by executing the gmx rms I have used 2 C-alpha
atoms at N-terminal and one C-alpha atom at C-terminal for least square
fitting and then calculated the RMSD for the rest of the C-alpha atoms.
Among the frames some frames got more than 2nm RMSD with respect to
starting structure. I have doubt here. 2nm means (20 Angstrom) is very
high, is it possible to get this mush deviation with respect to starting
structure? If it is yes, what is the reason for deviation?

Thanks in advance
Surya
Graduate student
India.