i have done md simulation with gromacs software but when i check the trajectories with vmd their is a break in dna strand even after repeated simulation with ligand? what will be the possible reason for this.
Most programs deduce biopolymer connectivity from interatomic distances. If the cut-off distance set in the program is too stringent, you see this apparent strand breaks. Check the manual of the program you are using to see how to adjust the cut-off distance.