GROMACS version:
GROMACS modification: Yes/No
Here post your question
gmx dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp_1.dat -xvg xmgrace
unable to plot dssp.dat file
What is it you want to plot? Have you tried using the -num output option?
i want to do secondary structure analysis, but unfortunately the output is in .dat format and i am unable to use the .dat to plot
could you elaborate the command?
You can open the .dat file in any text editor. But the information is not meant for plotting.
If you are interested in statistics over time, which could be plotted, the -num option will give that, e.g.: gmx dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp_1.dat -num num.xvg.
gmx dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp_1.dat -num num.xvg
Error in user input:
Invalid command-line options
Unknown command-line option -num
it gave an error
is there any way to perform secondary structure analysis using 2023.1
Sorry, I didn’t notice you are using GROMACS 2023. The dssp tool was changed in GROMACS 2024. You cannot get time based statistics (the num option) in GROMACS 2023.
You can still do secondary structure analysis. But then I’m not sure what you expect to plot.
i want to plot an image as attached… Can i use the present version .xtc and .tpr file in gromacs 2024 to plot?
That kind of time-based analysis should be possible in gromacs 2024, yes. And you can use the input from your current simulations.
i had run the command using 2024.1 but generated only LOOPS
how to generate time based analysis as previously shared image
Have you checked the file contents in a text editor? Have you tried xmgrace -nxy num.xvg (if you are using xmgrace)? I think it only plots the first set by default.
Great!