GROMACS version:2022 and 2023
GROMACS modification: Yes/No
Here post your question
hello all
i want to discuss about why my dna double helical structure is unwinding after simulation
i tried using different force fields like charmm36,charmm27, amber etc.,
can you guys please suggest me what kind of mistake i am making.
i am adding the reference picture
thanks in advance
Do you base your statement that it is unwinding on the RMSD plot? That just looks like it’s crossing the PBC boundary. See if
gmx trjconv -f <trj_file.xtc> -s <topol.tpr> -o <output1.xtc> -pbc whole
gmx trjconv -f <output1.xtc> -s <topol.tpr> -o <output2.xtc> -pbc nojump
helps.
See Terminology - GROMACS 2024.4 documentation for more info.
Thank you for your response sir,
yeah sir, Its crossing the PBC boundary, now i solved it sir.