Dear researchers
I am searching for a flexible and user friend software for plotting RMSD and RMSF curves except EXCEL. Could you suggest me a better software for my purpose. Thanks in advance for your response.
The data output is just going to be x & y axis data in most of the cases. So you can opt any plotting software which would be compact to you. Few common examples could be
MatLab
XMGRACE
GnuPlot
Grapher etc.,
It depends on what are you comfortable with. Xmgrace is a versatile software that you can use directly in order to plot from GROMACS files. If you are comfortable with little bit of codes then GNU plot, Python, Matlab are much useful. If you just want to do column drag and drop then qtiplot, sigmaplot, prism are excellent softwares.
The following program will be helpful to plot rmsd and rmsf http://thegrantlab.org/bio3d/webapps
In addition to rmsd and rmsf, there are several other trajectory analysis modules available.
Xmgrace is good. If you are using Desmond for your MD run, schrodinger suite has many modules to generate plots for your data.
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