Protein-DNA binding simulation

Hi Amo_18,
DNA is known to show base pair opening in the Charm36 force field. This was shown by Pan et al. (NAR, 2003) and by Galindo-Murillo et al. (Biochim. Biophys. Acta, Gen.Subj. 2015). One way to fix this is by constraining the first and last basepairs. I have some posts on this here (https://gromacs.bioexcel.eu/t/constraining-terminal-basepairs-in-dna/2549/9). You could also look at Sun et al., Journal of Physical Chemistry B, 2017, which is where I got the idea from.

Hope that helps! Good luck!