[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?
>

Have you watched the trajectory to see what happens?  Such a short peptide
may simply unfold and the RMSD would be reasonable in that case.

-Justin


Dear Justin,

The topology of the peptide is like thread, in other words the peptide is
already unfolded (it is intrinsically disordered region). while doing
simulations I have fixed the end residues. I have watched the trajectory in
VMD. And there is no problem in trajectory.


Surya
Graduate student
India.