[gmx-users] Regarding RMSD graph nalysis
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users