DNA MDS set-up

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Hi fellow GROMACSers,

I’m planning to perform molecular dynamics simulations of the interaction between a peptide and DNA, and I want to use Dickerson’s DNA structure for this purpose.
The PDB file for this structure is available, and I’ve downloaded it from RCSB.

When I open the file, I notice several positive charges around the DNA. Should these charges be removed before starting the simulation?

Also, should energy minimization and equilibration of the DNA structure be performed separately before studying its interaction with the peptide, even though the structure was obtained directly from RCSB?

If energy minimization and equilibration steps are required, can I use the same MDP files for DNA simulations as I use for peptide simulations (attached)?

minim.pdb.txt (1.0 KB)
npt.mdp.txt (2.5 KB)
nvt.mdp.txt (2.3 KB)

2

When I open the file, I notice several positive charges around the DNA. Should these charges be removed before starting the simulation?

This is up to you - do you think those charges are important for the stability of your DNA strand? If not, you can remove them. If you keep them, just make sure your system remains neutral by adding an appropriate amount of ions during the solvation step.

Also, should energy minimization and equilibration of the DNA structure be performed separately before studying its interaction with the peptide, even though the structure was obtained directly from RCSB?

If you want to study the interaction between the peptide and the DNA, i.e. they are in the same simulation box, then you should equilibrate them together. The point of equilibration is to reduce any unnecessarily large forces that might be introduced as you build your system.

Hope this answered your questions!

1 Like
3

Thank you so much for your detailed and helpful response!

I have a follow-up question related to Dickerson DNA, which has a -22e charge. In one study examining the interaction of a polycation with DNA, they obtained the DNA structure from RCSB and described their workflow as follows:

  1. They performed separate presimulations for structure relaxation in water with ions, running 100 ns for DNA and 50 ns for the polycation.
  2. Their simulation box included a double-stranded DNA molecule, a decameric strand of the polycation, water, 22 sodium ions, and 10 chloride ions for the polycation.

Does this imply that they removed the initial positive charges around the DNA? Additionally, does this mean they equilibrated the DNA separately before the main simulation?

I’m new to molecular dynamics simulation, so I’d greatly appreciate any advice or clarification you can offer!