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
difficult.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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