[gmx-users] Regarding RMSD graph nalysis
naga25sundar at gmail.com
Mon Sep 17 13:02:41 CEST 2012
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.
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