RMSD: gmx rms -s npt.tpr -f npt.xtc -o rmsd.xvg -tu ns

RMSF: gmx rmsf -f npt.xtc -s npt.tpr -o rmsfperresidue.xvg -ox average.pdb -oq bfactors.pdb -res

VMD?

Thanks Vijayan Ramachandran for your answer, but I want to draw plot from RMSD and RMSF tab file.

I believe what you want is to overlay both RMSD and RMSF output in a single graph?

If that is the case then you can use more or less what people have commented above, in addition to this you can also use qtgrace/xmgrace software to do overlay of two graphs or open two input files using the GUI and adjust the parameters (both x- and y-axis).

If you want to plot them individually you can do it the same way, else here is simple python script that can plot the gromacs xvg files (rmsd and rmsf) (only one file at a time though).

https://github.com/sanjaysrikakulam/gromacs_utility_scripts/blob/master/gromacs_scripts/plot_xvg.py

The common software is xmgrace

http://plasma-gate.weizmann.ac.il/Grace/

To make more advanced and customized plot, you can use gnuplot

http://www.gnuplot.info/

or matplotlib package of python

https://matplotlib.org/

Sorry to bother you guys but I need help to understand how to attain the "displacement trajectory " of a specific molecule.

In attachment figure can be seen.

Thanks in advance.

For obtaining the trajectory files and analyzing the simulations, HERO v3.0 is a great tool

https://heromdanalysis.wordpress.com/

Hai

For obtaining the trajectory files use QtGrace.

https://sourceforge.net/projects/qtgrace/

XmGrace/QtGrace software seems best for this purpose.