Fortran Simulation Output

Bead positions and identity

Periodically while running the simulation will take a save point and save the configuration of the polymer(s). These are saved in the data/ folder in files such as data/r100 where the number 100 denotes what savepoint it is. When using MPI to parallel temper, the data will be saved in the format data/r110v6 where 100 refers to the save point and 6 refers to the replica. This data will have three columns for the x, y, and z positions of each bead. If there are multiple polymers they will be printed one after the next with no delineation.

If WLC_P__SAVEAB is specified as true than data/r100v6 will contain a fourth column specifying the bead type. For two tail methylation profiles a value of 0 in this column refers to either tail bound by HP1, a value of 1 or 2 refers to one or the other tail bound by HP1, while a value of 3 refers to both tails being bound by HP1. If WLC_P__CHANGINGCHEMICALIDENTITY is true than a fifth column will specify the number of methylated tails (0, 1 or 2).

For example

21.702    39.628    14.415  0  0
21.715    39.617    14.892  3  1
21.205    39.449    14.758  3  2
20.718    39.472    14.672  3  2
20.463    39.763    14.803  0  0
20.209    39.667    15.418  1  0
19.888    39.643    14.826  2  0

Other files

If WLC_P__SAVEU is true then the orientation unit vectors for each bead will be stored as in files of a similar format to the positions. For example data/u100 or data/u100v6. If WLC_P__LOCAL_TWIST is also true then there will be three additional columns in the data/u100.

The file data/energiesv6 contains the various energies and corresponding coefficients. All energies are in kT’s. There is one line in this file per savepoint. The file data/adaptationsv6 contains the adapted window size, success rate, and so on the various move types. These files are useful for diagnosing problems and determining if the simulation is equilibrated.

A file data/repHistory contains various information about replica coupling if it is in use.


We provide visualization code based on pymol. To run, navigate to ‘visualization/polymer_mole’, enter the savepoint and other settings into and then type python3 This will require both python3 and pymol. The way it works is that the output described above is converted into a pdb file which is then passed to pymol. Various sets of settings that have been used in the past are included in To use one of thes set image to the name of the corrisponing set.

If closePymol is set to true in run_visualization than the output will be saved to the data/ directiory. By editing the line for rep in … you can save many snapshots.