I want to calculate rmsf between both time and residues. Is there any way to calculate it using Gromacs?
g_rmsf has the -b and -e options that allows you divide your trajectory into whichever time frames you want to compute your RMSF values. The -res option give you RMSF values per residue. The outputs are in .xvg, convertible to .csv. you can then use excel or any similar program to plot your data. A script to write out all xvg outputs into a common .xvg file is useful.
g_rmsf has the -b and -e options that allows you divide your trajectory into whichever time frames you want to compute your RMSF values. The -res option give you RMSF values per residue. The outputs are in .xvg, convertible to .csv. you can then use excel or any similar program to plot your data. A script to write out all xvg outputs into a common .xvg file is useful.
In case of OS Linux Ubuntu first install xmgrace by using command sudo apt-get install. Then try thes commands:-
xmgrace in terninal g_rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
xmgrace -nxy rmsf.xvg
:)
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