[gmx-users] structural clashes make the structure look like broken?

[sunyeping]

Dear all,

I am doing MD of a protein-DNA complex. There are some structural clashes between the DNA and the protein, but both of them look complete (Please see the figure at https://drive.google.com/file/d/1K7xiv4Lf7UEggNIykWxXX2WRtclJxv2q/view?usp=sharing. The clashes are indicated by the red arrows). However, after I prepared the gro file with pdb2gmx, did energy minimization, when I did nvt and npt equilibrium, I found that one of the  DNA chain became broken (Please see the figure at https://drive.google.com/file/d/1FtGPWjhnEqbWchmQaWEA3YpSqWca5Eyd/view?usp=sharing. The broken site of the DNA is indicated by the red circle). 

I think the break in the DNA is caused by the structural clash between the DNA and the protein and the clashing atoms can not be shown in the visulization software (such as pymol and vmd). 

I am wondering whether the structural clashes will finally disappear in a prolonged simulation or it will kept. If the MD simulation will not remove the structural clashes, I should give up it. What do you think? Do you have any idea of removing the structural clashes in the initial structure?

Best regards.