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Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

The Mol_Analysis.py script is a script that assist in the basics analyses of MD simulations with GROMACS tools. It provides both the raw output data and different pdf reports with the summary of the analyses. The pdf are produced thanks to matplotlib.

To run Mol_Analysis.py, the user needs  a config file in which to specifity the input files and the group definition for GROMACS index files. An example of config file and its syntax is reported in this repository (config.cfg). 

In particular Mol_Analysis.py allows the following steps/analyses: i) calculation of minimal distance between the protein and its periodic image to check PBC issues using g_mindist, ii) centering of the trajectory in the box for analyses, iii) root mean square deviation, iv) radius of gyration, v) root mean square fluctuation, vi) comparison of different trajectories

More information on the options and command line here:

usage: Mol_Analysis.py [-h] [-f config.cfg] [-n] [-nomindist] [-nopdb] [-v]
                          [-nt N] [-local] [-nogroup] [-begin BEGIN]
                          [-end END] [-large]

This is a script that can assist in plotting data of MD simulations with matplotlib.

optional arguments:
  -h, --help     show this help message and exit
  -f config.cfg  Specify the input config file
  -n             Dryrun, no gromacs analysis are run
  -nomindist     No gromacs mindist analysis are run
  -nopdb         No .pdb movie are output
  -v             Verbose mode
  -nt N          Number of threads/cores for paralelization
  -local         Locate plots in folder of script
  -nogroup       No groupplot
  -begin BEGIN   Begin from time X (fs)
  -end END       End at time X (fs)
  -large         Can plot 9 plots
  -splitlen      slen Lenght of timewindow for RMSF calculation (in ns, default=10 ns)
		 if multiple times need to be calculated then separate with a comma

COMMAND LINE (if you run in remote use ssh -X -Y):

python -u Mol_Analysis.py -f config.cfg

python -u Mol_Analysis.py -n  #if the calculation was already carried out but the plots were not generate - this will read the output files and generate the report

NOTES:

If in running the script you have an error message related to the name of the gromacs tool, try to  set the function renaming to False on line 30 and run again. It is a temporary fix. We are working on it.

When using the Mol_Analysis.py for publication please cite:

Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon, Elena Papaleo*,
Analyzing biomolecular ensembles. Methods Mol Biol. 2019;2022:415-451. doi: 10.1007/978-1-4939-9608-7_18.

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