I have been using QwikMD/NAMD to run MD simulations, and for each setup I run three simulations to have replicate results. Now, I would like to plot the results from the three trajectories, along with the average result of the three, on the same plot. For example, for the RMSD or RMSF values, I can plot each trajectory individually using the Basic Analysis and Advanced Analysis tabs within QwikMD. However, I cannot find a way to plot all three trajectories on the same plot in QwikMD or VMD.
I have attached an example of the type of plot I would like to create, where the replicate results and average results are all shown on the same plot (for interfacial SASA in this case). What software can be used to create such a plot? GUI options are preferred, but I would like to explore all options.
Do I export each plot I have created in QwikMD in a certain format in order to use matplotlib to combine them? The plot export options I can see are PostScript, Xmgrace, ASCII matrix, and ASCII vectors.
Hello Christos Eu
what Martin meant is plotting/visualizing the data with python using the matplotlib package.
There would also be options with other programming languages, packages (for these languages) or programs (plotly package in python next to matplotlib, R programming language with e.g. the ggplot2 package,... gnuplot,... or Xmgrace what you mentioned, but with fewer possibilities)
For all these options you would need the raw data (x and y values for each point, e.g. time vs. RMSD for every simulation time step), not the plots!
Then you can also manipulate the data, e.g. calculate the average and finally plot whatever you want.
All these plotting options would also allow you to change the design how you wish. However, if you never used them, it might be difficult to get the first plot or even loading the data.
I can finally just regret to say that I have never used QwikMD and so I do not know how to get access to the raw data. You should still ask someone who has experience with that simulation software.
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