I have performed MD simulation run using GROMACS for a mutant protein (50ns), now to analyze trajectories generated for PCA, RMSD, RMSF value and other calculation studies, how can I proceed?
In gromacs, analyzing tools are available. you can find gmx rms for RMSD, gmx rmsf for RMSF..like this. And you can also visit gromacs tutorial website http://www.mdtutorials.com/gmx/.
HeroMDAnalysis is a tool for analysis of gromacs based MD simulation. Its free and support analysis of various parameters such as RMSD, RMSF, RoG, SASA, Free energy of Solv, H-bond contacts, Thermodynamic paramters, PCA Analysis. Its very simple, Graphical User Interface tool with no prior knowledge of command line interface required. Please visit www.heromdanalysis.wordpress.com for more information about this tool.