DNA TOP file

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Hi, I hope youre’doing well.

I am studying peptide/DNA interactions as well as DNA/membrane interactions using GROMACS. My DNA structure consists of two strands, and I am unsure whether to treat the DNA as a single molecule or as separate chains in my simulations.

Should I define the DNA as a single molecule in the topology file and use tools like pdb2gmx -merge interactive to merge the strands together? Or would it be better to treat the DNA strands as separate chains?

I want to ensure that I handle periodic boundary conditions correctly and avoid any broken molecule appearance in the trajectory. Which approach would be more appropriate for these types of simulations?

2

hello,
Hello,

The separation of two strands of DNA is because of PBC. If you consider a very, very, very big box, it is computationally expensive, and you will not see any separation. You can follow my previous discussion for the correction of two separate DNA strands. Putting them in an ITP is useful when you want to apply a restraint to DNA, which must be in one ITP. Furthermore, if there is a covalent bond between DNA and protein, you must merge the ITP.

3

Thank you so much for your response!