# Protein-DNA binding simulation

**URL:** https://gromacs.bioexcel.eu/t/protein-dna-binding-simulation/3733
**Category:** User discussions
**Created:** [February 23, 2022, 2:01pm UTC](https://gromacs.bioexcel.eu/t/protein-dna-binding-simulation/3733 "2022-02-23T14:01:15Z")
**Posts on this page:** 1
**Showing post:** 4

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### Author: ![kandresen](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/kandresen/32/747_2.png) [@kandresen](https://gromacs.bioexcel.eu/u/kandresen)
#### Post date: [March 1, 2022, 5:58pm UTC](https://gromacs.bioexcel.eu/t/protein-dna-binding-simulation/3733/4 "2022-03-01T17:58:37Z")

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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](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!

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