REMD implementation using oxpy

Script requirements

• Please use the latest version of oxDNA.
• The script requires
  • mpi4py to parallelise the computation
  • tqdm to estimate the run time (optional package: if not found no progress meter will be shown and a warning will be issued)

Input file requirements

• Regular oxDNA input files should work, but note that the following parameters get overwritten by oxpy:

    lastconf_file 
    trajectory_file 
    energy_file 
    CUDA_device
    T

• For CUDA runs the script assumes that the number of available GPUs is at least equal to the number of temperatures you are scanning and that the devices are available sequentially.
• The following parameters are specific to a REMD run.

    pt_temp_list =  290K, 315K, 330K, 345K
    pt_move_every = 5000 

where:

• pt_temp_list is the list of sampled temperatures.
• pt_move_every is number of iterations between the temperature exchange tries.

REMD run

To run a REMD simulation execute the following commands:

./clean.sh

mpirun -n 4  python3  remd.py  input_md

python3 reshuffle.py input_md history.json reshuffled

• clean.sh cleans up the simulation folder.
• remd.py runs the simulation.
• reshuffle.py restores the temperature trajectories.

Note that -n 4 corresponds to the number of temperatures you are sampling. The remd.py script prints out the estimated run time and the exchange rates.