Dear GROMACS expert,
I am currently having trouble to analyse the results from my simulations. After processing the output files using this command,
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center
and calculate the RMSD with this
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
I noticed that my graph plot did not start from 0ns, but started from ~90ns. My simulation time was 120ns, and how do I plot the graph of the RMSD from 0ns?
Thank you in advanced
Dear Nur Arshad,
To select the desired time intervals in GROMACS commands, you need to use the options -b (start time) and -e (end time). However, if the command is executed without these options, the analysis will start from the beginning of the MD simulation time.
Therefore, it is possible that there might be an issue with your md.xtc file, resulting in the analysis being performed only from 90 ns onwards. If possible, please upload the output file of the gmx rms command (rmsd.xvg) and a screenshot of the terminal during the analysis process for checking.
Dear Hamed Zahraee , thank you for your response.
I think I managed to concatenate my trajectory files output from the simulations using the gmx trjcat after I noticed that I have a few .xtc files output. Since from the .log files of each of the .xtc file indicated that, the first file starts at 0ns and stops at 1000ns, the second one starts at 1000ns and stop at 92680ns, and the last file starts at 92670ns and ends at 120000ns.
However, the thing is now, my plot does not look as nice as the other RMSD plots that I have seen and I am not sure what can I interpret from my simulation.
I have attached the RMSD plot, if you can give any comment or suggestion, I will be really grateful. Thank you.
You need to remove the PDB effect from the trajectory, then it will look as expected.
Use gmx trjconv with different combinations to get the desired results.
Dear Nur Arshad,
This is a PBC effect shown for the first part of the simulation up to 92 ns. Remove the PBC effect for the .xtc files from 0 to 92 ns. You can find a similar problem in this link:
https://www.researchgate.net/post/Does-anyone-have-experience-with-unconventional-RMSD
Thank you so much for your suggestion and advice Hamed Zahraee Ayaz Anwar.
I think I've managed to get rid of the not pretty plot at the first frame using the -pbc nojump as below.
Is this considered a good RMSD value for the complex? As I've read that RMSD should have minimal fluctuation to be considered that the protein complex is flexible and stable.
I suggest that in order to achieve a stable state for the complex, the MD simulation should be continued for a minimum of 200 ns
Hi Hamed Zahraee, since I have been renting out the server to run the simulations as I don't have the resources, I am afraid I won't be able to run a longer simulation as the rental period is over.
Do you have any other suggestions? Thank you.
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