Molecular Dynamics trajectories for "New Insights into the Structure and Dynamics of the Epigenetic Modifications on DNA"

Molecular dynamics simulations on DNA duplexes with sequence: Strand 1: 3'-CCCGGGXGTCCC-5'Strand 2: 5'-GGGCCC2ApCAGGG-3' where X=T,C,mC,hmC The non-standard bases are: 2Ap: 2-aminopurinemC: methyl cytosinehmC: hydroxymethylcitosine Simulations are conducted in water at room temperature for 100ns using a time step of 1fs (with one test using 2fs, which delivers equivalent results). The software used to conduct the simulations is Gromacs 2021.4 The upload material includes, for each system: The initial (equilibrated) configuration with DNA, water and ions The trajectory (excluding solvent and ions) in xtc format Topology files (top and itp) Parameter file (mdp) There is one run for each system (with a time step of 1fs), except for X=, where a duplicate run exists with a time step of 2fs. The trajectories have been analysed in an accepted paper published in RSC Chemical Biology (pending DOI), with title "New Insights into the Structure and Dynamics of the Epigenetic Modifications on DNA"