I performed docking for a complex of Ab-Ag and its mutants, then I did molecular dynamic (Gromacs 5.0.4) for results of docking ( wild and mutants). Now, RMSD of mutants is stable but wild type has huge fluctuations. Although the RMSD of wild type complex before docking was stable. Do you anyone know about the cause of difference? And how can I compare wild and mutant RMSD?
RMSD is a metric that tells you very little useful information. If the fluctuations truly are "huge," as you say, sudden spikes, etc. then this just means you haven't corrected your trajectory for jumps across periodic boundaries. The first step of any simulation analysis is, of course, to watch the trajectory, in which case such behavior would be plain. Otherwise, perhaps it is just a loop region (or more than one) that is just flopping around, in which case, again visualization will tell you what's happening.
RMSD is a metric that tells you very little useful information. If the fluctuations truly are "huge," as you say, sudden spikes, etc. then this just means you haven't corrected your trajectory for jumps across periodic boundaries. The first step of any simulation analysis is, of course, to watch the trajectory, in which case such behavior would be plain. Otherwise, perhaps it is just a loop region (or more than one) that is just flopping around, in which case, again visualization will tell you what's happening.
Thanks Justin for your answer. I checked trajectory files with Vmd and as you said flopping was happened at loops of antibody.
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