maybe you need the "-pbc mol" or "-pbc nojump", assuming that the two DNA strands are separated due to PBC.

Ricardo J Ferreira

Hello,

Thank you for your reply. I think it is because of PBC. One thing that is not clear to me is whether using -pbc cluster can change or have any effect on the structure of DNA? I found a tutorial on using -pbc cluster for DNA at this link.

http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-martini-dna-gmx5

I think there are some ways to correct the PBC.

Yes, your approach is mostly correct, but a small clarification:

So, your procedure looks good, and visualizing with file-cluster_center.xtc is appropriate.

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.