DND1_RNA_MD_simulations_part1

The NAMD input and output files for the equilibration and production runs are provided in "inputs.tar.gz" and "outputs.tar.gz". The simulations of the DND1-RNA (RRM1-RRM2-RNA) complex and the free DND1 protein (RRM-RRM2). For each system, there are 3 independent simulations (m1, m2, m3 in .netcdf format) started with a different initial structure. To load the files in a visualisation program first the AMBER topology .prmtop file is needed and then a trajectory file. Example for VMD vmd -parm7 .prmtop -netcdf .netcdf