CG chromosome in metaphase (Naumova et Al 2013)
This is the structure of a chromosome in metaphase, as predicted by the "two-stage" model used to explain the results of a recent chromosome capture experiments on metaphase cells. (Naumova et Al Science, 2013). It has been rendered to make the interior more easily visible. (This model was described in the supplemental materials section of that paper, in the section titled: "Two-stage process: linear compaction - axial compression".) This was my attempt to implement that model in LAMMPS using moltemplate. (This simulation was originally run using other software.)
CG chromosome in metaphase (Naumova et Al 2013)



This example can be downloaded. The input files are located in the "coarse_grained/" subdirectory of the examples distributed with moltemplate.

3-D graphics generated by VMD & topotools