Running the MD simulation

The MD simulation is most commonly run on a computer cluster. This step requires two files from previous steps:

  1. The protein structure (a .pdb file)

  2. The CV indices (a .npy file)

The two input files should be uploaded to the cluster. Our package provides a fast way to run the simulation using the OpenMM package.

Note

The user is also welcomed to use their own method or software to perform the simulation. The end product of the simulation should contain:

  1. A trajectory file (a .xtc file)

  2. A CV file (a .dat file)

Tip

It is recommended to first check if your OpenMM is correctly installed with GPU support. To check, simply run in the GPU cluster: python -m openmm.testInstallation. More details can be found at http://docs.openmm.org/latest/userguide/application/01_getting_started.html

The following code snippet shows how to run the simulation:

import af2rave.simulation
import numpy as np

filename = "sample_box.pdb"
idx = np.load("cv_indices.npy")

ubs = af2rave.simulation.UnbiasedSimulation(
    filename, list_of_index=idx,
    xtc_file=f"sample.xtc", xtc_freq=50000,
    cv_file=f"sample.dat", cv_freq=500
)

ubs.run(50000000)
ubs.save_pdb(f"restart.pdb")
ubs.save_checkpoint(f"restart.chk")

This can be put in a script and submitted to the cluster. The simulation will run for 100 ns and save the trajectory in sample.xtc and the CVs in sample.dat. The simulation can be restarted from the checkpoint file restart.chk.