Project_rNA-MD

1. Input files in the repository:

main files:

freqs_all.txt: frequencies of NAC (odd row) and energy gap (even row) of each model.

ampl_all.txt: amplitudes of corresponding frequencies for NAC (odd row) and energy gap (even row) of each model.

run_namd.py: the code to execute the NA-MD run.

ham.py: the module to generate the model Hamiltonian.

2. The example output directory:

res_model1_102_100000_1000

The directory contains the data of Model 1 (model1) with NAC scaled by 0.2 (102). The length of the original dataset is 1000 fs (1000), we repeat it 100 times to get the total length of 100000 fs (100000).