Greeting 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 http://imageshack.us/photo/my-images/840/rmsd.png/ 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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