[gmx-users] Regarding RMSD graph nalysis

Justin Lemkul jalemkul at vt.edu
Mon Sep 17 14:10:27 CEST 2012

On 9/17/12 7:02 AM, naga sundar wrote:
> 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.

It sounds to me like your trajectories haven't correctly accounted for 
periodicity.  g_rms does not elegantly handle sudden jumps across the box.  You 
will need to work with trjconv.  Usually a simple trjconv -pbc mol -ur compact 
-center does the trick for a simple protein, but for complexes it is often more 




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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