Making DNA whole in a triclinic box

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1

GROMACS version: 2016.4
GROMACS modification: No
Here post your question :

Hi ALL,

I am simulating a modified DNA in a triclinic box. The modified DNA was prepared using CHARMM-GUI and simulated in water+ions (150 mM KCl). I see the DNA is breaking within the first few steps of the MD. I tried using gmx trjconv with -pbc whole , -nojump and -cluster but the DNA still looks fragmented when I upload the modified trajectories in VMD. I am attaching the md.xtc and md.tpr for your reference. Can you help me? I am currently unable to find a suitable workaround for proper visualization of the trajectory in VMD after removing PBC effects. Also, I don’t know if this may happen due to faulty topology parameters .
[MD trajectory]
https://drive.google.com/file/d/1_zHxTreN6L9Xn5Xh6-y1fnEdurPQtlrZ/view?usp=sharing

[MD tpr]
https://drive.google.com/file/d/1CIMzh4MuSSUc3A7WKuEqfJwd-f9dAisW/view?usp=sharing

Thanks in advance
Soumadwip

2

Hi,
The option whole only makes broken molecules whole. Usually DNA double strands (you did not specify, but I assume that your DNA is double stranded) are defined using a itp file for chain and not as 1 molecule in topology. That may cause that the results is not the desired one.
what about to try 1) -nojump 2) -center

here you can find more on trajectory post-processing Terminology — GROMACS 2021 documentation
Best regards
Alessandra