Visualising Molecular Dynamics Analyses

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.


Version: 1.0.1 Date: 2017-07-04

o fixed some typos in the manual pages o added vignette (publication) o added special input support for function "load_timeseries()" to be able to load multi-column timeseries data

Version: 1.0.0 Date: 2017-02-24

o fixed issue with proper residue display when sub-selection was done in function 'dssp()' o fixed issue with bin-expansion in function 'load_noe()' o removed unnecessary input parameters from several functions o added 'stride' to function 'load_dssp_ts()' o changed parameters of function 'load_rmsf()' o renamed functions 'load_dssp_summary()' and 'dssp_summary()' into 'load_dssp()' and 'dssp()', respectively o added additional box lines to function 'ramachandran()' for 'plotType = "comic"' o changed colour coding to be more consistent in function 'ramachandran()' o added 'barScaleFactor' to function 'dssp_ts()' to account for the possibility that very small peptides might be plotted o added GROMACS support for functions: 'load_dssp()', 'load_dssp_ts()', 'load_hbond()', 'load_hbond_ts()', 'load_clusters()', 'load_clusters_ts()', 'load_ramachandran()' and 'load_xrmsd()' o added AMBER support for functions: 'load_rmsd()', 'load_ramachandran()', 'load_dssp()', 'load_dssp_ts()', 'load_hbond()', 'load_clusters()', 'load_clusters_ts()', 'load_rmsf()' and 'load_xrmsd()' o added function 'load_XPM()' to load "X PixMap" data as commonly produced by GROMACS o added functions 'find_Nth_occurrence()', 'split_GROMACS_atomnames()' and 'split_AMBER_atomnames()' to the collection of helper functions o added parameter 'showMultipleInteractions' to function 'hbond()' to represent multi- or hybrid hydrogen bond donors and acceptors o fixed time-axis issue in functions 'rmsd()' and 'rmsf()' o changed all names on example input files according to convention

Version: 0.3.1 Date: 2016-04-28

o added 'printErrors' flag to function 'TIcurve()' o added 'errorBarThreshold' flag to function 'TIcurve()' o fixed bug in function 'ramachandran()' for type "fancy" o added return information to functions where appropriate o fixed 'xrmsd()' ellipsis o changed some phrases and the title

Version: 0.3 Date: 2016-02-15

o added multiple vector selection by hydrogen bond identifiers to function 'hbond_ts()' o added argument 'printValues' functionality to function 'TIcurve()' o removed hard-coding for the filenames of function 'load_dssp_ts()' o included new functions 'load_timeseries()' and 'timeseries()' o added argument 'legendPosition' to functions 'rmsd()' and 'rmsf()' o added labels for axes for function 'xrmsd()' o renamed title ("Analyses") to comply with the publication title

Reference manual

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1.0.1 by Christian Margreitter, 2 years ago

Browse source code at

Authors: Christian Margreitter [aut, cre] , Chris Oostenbrink [aut]

Documentation:   PDF Manual  

GPL-3 license

Depends on methods, MASS, RColorBrewer, gplots, gtools

Suggests R.rsp

See at CRAN