Contains MD-simulation code written to simulate our model of Condensin using OpenMM.

This python script can be used to simulate equilibirum properties of Condensin and DNA by changing the number of steps Condensin spends in either B-state or O-state. The MD simulation is written using the OpenMM package. The script takes bond-length, bond-angle and initial particle positions as input. Finally it produces a trajectory and topology file as an output. The trajectory is written in dcd format and can be read using VMD. The trajectories used in the main text and supplementary material can be found at: https://drive.google.com/drive/folders/1jCMMY0Joqomp7ZuXkdKahOTSRJBI3Ujk

• Basic underderstanding of bash, python and how to use terminal
• Python 3.7+
• OpenMM version 7
• Python package installer conda, to install OpenMM.
• Linux, Mac or Windown OS

• For general OpenMM installation instructions see http://docs.openmm.org/latest/userguide/application.html#installing-openmm.
• We used conda install -c conda-forge openmm cudatoolkit==10.0
• Clone/download the repository
• Move to the downloaded folder.
• Run the following script in a bash window capable of running python, python CG_model_Condensin_Elbow.py

• coord_start.pdb - Contains initial starting structure
• bondList.dat - Contains list of bonds and bond-lengths
• DNAangles.dat - Contains list of bond-angles used in DNA
• CondensinAngles.dat - Contains list of angles used in Condensin model
• particleList.dat - Contains particle names and sizes

• topology.pdb - Contains a topology file to be used with dcd file
• output.dcd - Contains output trajectory in dcd format
• The bash window will also print all the energy values for each frame in the trajectory. This output can be redirected to a file if necessary.

Example Input: python CG_model_Condensin_Elbow.py

Example Output:

Loaded everything

Setup forces

#"Step" "Time (ps)" "Potential Energy (kJ/mole)" "Total Energy (kJ/mole)"

10000 39.99999999999959 710.12109375 936.8952330127358
20000 80.00000000000584 754.1318359375 1012.8524764608592
30000 120.00000000005473 790.8985595703125 1044.234991952777
40000 159.9999999999899 748.962646484375 1043.2672696188092
50000 199.9999999998967 765.4717407226562 1036.2402911083773
60000 239.99999999980346 747.9782104492188 1005.5008238162845
70000 279.99999999988074 767.0703125 1018.1886996394023
80000 320.00000000007174 796.067138671875 1042.7340556159616
90000 360.00000000026273 776.9962158203125 1050.8454275801778
100000 400.0000000004537 768.4482421875 1073.195808040211
110000 440.0000000006447 1028.3388671875 1390.8749343901873
120000 480.0000000008357 955.2681274414062 1287.7714983522892
130000 520.0000000010267 959.2990112304688 1271.9728351458907
140000 560.0000000012177 949.7865600585938 1213.0935844928026
150000 600.0000000014087 916.6130981445312 1194.2609043851262
160000 640.0000000015997 926.5377197265625 1191.74046555534
170000 680.0000000017907 960.9150390625 1249.244273437187
180000 720.0000000019817 947.8404541015625 1243.5862293243408
190000 760.0000000021727 926.4295654296875 1208.819168381393
200000 800.0000000023637 917.871826171875 1203.7580848727375
210000 840.0000000025547 811.3917236328125 1119.5756307952106
220000 880.0000000027457 782.7474365234375 1067.1339964009821
230000 920.0000000029366 787.230712890625 1054.1576135675423
240000 960.0000000031276 806.4061889648438 1092.6120233759284
250000 1000.0000000033186 789.201171875 1084.6818463131785
260000 1040.0000000030548 796.983642578125 1079.317869907245
270000 1080.000000002109 770.011474609375 1036.6852607652545
280000 1120.000000001163 801.9671630859375 1060.0420704837888
290000 1160.0000000002171 750.493896484375 1014.5487550422549
300000 1199.9999999992713 761.3817749023438 1019.675249459222
Time Elapsed : 41.842265129089355