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).
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
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 run_visualization.py and then type python3 run_visualization.py. 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 run_visualization.py. 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.