[gmx-users] DNA strands disconneting from each other along MD simulations

[Tanos C. C. Franca]

    Hi GROMACS users !
    I am using amber force field to perform 10 ns MD simulations of a 
DNA dodecamer docked with small molecules in order to check if these 
molecules stay between the strands interacting with the nucleotides, 
but, after the simulations, I've observed that sometimes the DNA strands 
disconnect totally from each other and some ns later get together again. 
I initially  thought that it would be a bug of the VMD software (that I 
used to visualize de MD results) but when I analysed the temporal RMSD 
plots, I've saw big peaks at that times the DNA strands separated from 
each other. Does someone knows why the DNA strands are disconneting from 
each other and how to fix it ?
    With the best regards,
    Tanos C. C. Franca.
    Rio de Janeiro - RJ
    Brazil.