[gmx-users] equilbium convergence and RMSD structure

larif sofiene larifsofiene at gmail.com
Tue Nov 1 00:56:25 CET 2011

I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated
forms has converged to equilibrium and simulation is suitable for analysis.
The 4 MD simulations are done in cubic water volume, 500 ps of steepest
descent minimization , with 100 ps of NVT ensemble and 100 ps of NPT
ensemble , reaching for all of them their desirable value and being stable
over time
When doing an MD production for 10 ns with those parameter :
* constraint_algorithm = lincs
* constraints    = all-bonds
* coulombtype    = PME
* tcoupl        = V-rescale
* pcoupl        = Parrinello-Rahman
* pcoupltype    = isotropic

leading to those RMSD
the first one on the upper left is wild type other are mutants.
my question is are my system in equilibrium despite those 2 spikes on 7 and
9 ns in WT RMSD , knowing that all the 4 MD had stable radius of gyration ,
stable potential energy , stable H bond forming and dissociation over time
and reasonable H bonds under structural analysis, and if so, does those
spikes mean structural changes in flexible regions that i must check for
with RMSF ?
Thanks in advance for responding :)
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