Incommensurate structure of Hexamethylenetetramine suberate (C6H12N4)(HOOC-(CH2)6-COOH) has been solved from single crystal x-ray diffraction data. A molecular dynamics simulation of this system was carried out from 15 K to 580K. A second-generation consistent forcefield (CFF) and a compensating pressure tensor field were used to describe the interactions between atoms and to account for deficiencies in the forcefield. Starting from the experimental 298K structure, the phase transitions were investigated over an extended temperature range. A high symmetry commensurate structure exists at temperatures between 410K and 290K. For temperatures lower than 290K, a new periodicity appears in the structure. The system reaches a low symmetry lock-in phase at about 150K. An incommensurate structure appears between the high and low symmetry phases between 290K and 150K. The new periodicity associated with the incommensurate modulation is due to the appearance of additional long range ordering of the carbon chains. The present simulation not only reproduces well the experimental x-ray diffraction results but also gives new insight into the origin of the incommensurate behavior.