GROMACS version: 2020.2
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Dear all,
I am running a simulation of a complex molecule. it has two chain. When I calculated the rmsd and found that rmsd value shoots up at 16ns and 25ns. In corresponding PDBs two chains are far apart, out of the box. Is it artifacts? if the complex broke at 16ns why it re associates ? How can I fix it? Thank you
This is a periodicity artifact. Recenter with trjconv.
Dear Dr Jalemkul,
Following your advice, I combined the xtc file using âgmx trjcat -f step5_*.xtc -o combined.xtc -settimeâ
then i tried to remove PBC using " gmx trjconv -s step4.0_minimization.tpr -f combined.xtc -o md_0_1_noPBC.xtc -pbc mol -center"
Then i calculated the rmsd using âgmx rms -s step4.0_minimization.tpr -f md_0_1_noPBC.xtc -o rmsd1.xvg -tu nsâ
but still its not centered. the two chains are far apart and rmsd is absurd for these frames. Am I doing anything wrong?
Thank you
Veeru
http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow
For multiple chains, center on one of them, but you will have to do other steps first as suggested in this link.
Thank you Dr Jalemkul. As I am new to Gromacs. I really couldnât follow the steps given in the link. Is it possible to get set of commnads. Sorry for the trouble.
Best regards
Veeru
You will learn lots by reading the trjconv help information, which describes everything mentioned in that link :)
Dear Dr Jalemkul,
I mange to fix pbc issue. Thanks for your help. I got another question. what is criterion to decide the simulation has saturated? Is the simulation below saturated already at 40ns? as the rmsd plot is flat though i still see small bumps
Are you talking about convergence? RMSD doesnât tell you that. Itâs a degenerate metric. You need to examine all relevant structural properties of interest and they should be statistically invariant over time.
Hello there,
i have the same problem ( i have RMSD shoot-ups and my protein complex comes out of the box) how can i fix it? shall i do all the steps from beginning?
i have check the trajectory file with PYMOL itâs fine until 80 ns how can i fix it?
i would be really glad if you help me thanks.
hello,
may i ask you how could you over com your issue with your RMSD shoot-ups? was it from complex coming out of the box?
thanks.
From the plot it definitely looks like a problem with PBCs. You have to âclean-upâ the trajectory with some pre-processing tools like gmx trjconv.
thanks for your reply, by âclean-upâ you mean what, Iâm not sure if i get your point.
I have realized that itâs about PBC but Iâm not sure how to overcome it.
Iâve tried PBC -no jump and other PBC conditions but i think Iâm doing something wrong cause I donât get reasonable result from my system.
thanks for your guidance.
With clean-up I mean pre-process the trajectory for data analysis. Sometimes it is not needed and sometimes, like in your case, is mandatory, depending on the analysis you want to carry out.
You have to remove the effect of PBCs. You have to play around with trjconv and various flags like -pbc mol, -pbc nojump, and some centering, probably. What do you mean with âreasonable resultsâ? The spikes you have in the plot you posted are clearly artifacts. Then, whether the RMSD values are reasonable or not (spikes excluded), that I do not know.
Hello again and thanks for your reply, Iâve tried few options around trjconv as you said in some cases RMSD goes around 22 A and in some cases it plays around 1 A but the box shatters Iâm not sure if itâs alright or not?
i want to get these data: RMSD, RDF, RMSF, binding energy and if possible SASA. I would be really glad if you help me out.
P.S: when i tried -nojump sol of box get disrupted.
What do you mean with the box shatters?
solvent doesnât look like a proper box.
This is because you used the flag -pbc nojump, which unwraps the PBCs and avoids jumps between sides of the box (the reason why you had that artifact in the RMSD plot). This is also reported in the trjconv manual
