Visualising Molecular Dynamics Analyses
Loading function for rmsf()
Loading function for thermodynamic integration function TIcurve()
Loading function for timeseries()
Loading function for xrmsd()
Internal functions for MDplot
Arguments for bash script interface
Cluster bar plot
Cluster timeseries plot
DSSP plot for secondary structure elements (proteins)
DSSP timeseries plot for secondary structure elements (proteins)
Plot hydrogen bond summary
Plot hydrogen bond timeseries
Loading cluster information
Loading timeseries cluster information
Load DSSP information
Load DSSP timeseries
Loading hydrogen bond data
Loading hydrogen bonds timeseries
Loading NOE violations
Load dihedral information (Ramachandran plot input)
Loading function for rmsd()
Plot NOE violations
Ramachandran plot for two dihedral angles
Root-mean-square-deviation (RMSD) plot
Root-mean-square-deviation (RMSD) average plot
Root-mean-square-fluctuation (RMSF) plot
Thermodynamic integration plot
General timeseries plotting function
Function to translate between canonical and GROMOS amino acid abbrevia...
XRMSD plot in heatmap style
Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis. Currently able to load GROMOS, GROMACS and AMBER formats, respectively.