Analysis

In this chapter different ways of analyzing your trajectory are described. The names of the corresponding analysis programs are given. Specific information on the in- and output of these programs can be found in the tool documentation here. The output files are often produced as finished Grace/Xmgr graphs.

First, in sec. Using Groups, the group concept in analysis is explained. Selections explains a newer concept of dynamic selections, which is currently supported by a few tools. Then, the different analysis tools are presented.

• Using Groups
  • Default Groups
  • Selections
• Looking at your trajectory
• General properties
• Radial distribution functions
• Correlation functions
  • Theory of correlation functions
  • Using FFT for computation of the ACF
  • Special forms of the ACF
  • Some Applications
• Curve fitting in GROMACS
  • Sum of exponential functions
  • Error estimation
  • Interphase boundary demarcation
  • Transverse current autocorrelation function
  • Viscosity estimation from pressure autocorrelation function
• Mean Square Displacement
• Bonds/distances, angles and dihedrals
• Radius of gyration and distances
• Root mean square deviations in structure
• Covariance analysis
• Dihedral principal component analysis
• Hydrogen bonds
• Protein-related items
• Interface-related items