AnalysisΒΆ
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
- Looking at your trajectory
- General properties
- Radial distribution functions
- Correlation functions
- Curve fitting in GROMACS
- 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