[gmx-users] Regarding RMSD graph nalysis

[naga sundar]

Dear gromacs users

I run  20 ns MD simulation for protein mutant complexes. In RMSD analysis
at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7
nm and immediate fall was observed.

I rerun the 20 ns simulation for the same molecule with same procedure.
While analyzing the RMSD sudden increase in the deviation was observed (0.2
nm to 1.7 nm) at the simulation period of ~12 ns.

So i want to know  the reason

For sudden rise and fall in RMSD values.

Next, in first MD run this deviation was observed at ~9 ns (0.2 nm to 1.7
nm) but while rerun the molecule with same procedure this deviation was
observed at ~12 ns.
-- 
Regards
N.NagaSundaram