Simulation Data for Pairs of Small Peptides

Umbrella sampling between two peptides covering distances from 3 A to 30 A. The distances are measured between the centers-of-mass of the "saved_atoms" in peptide 1 and 2.

Data is located in /import/a12/users/kraemea88/two_peptides.

Units

The coordinates in data files are in units of nanometers. The forces are unbiased forces in units of kJ/mol/nm.

Loading and processing Data

Processed all-atom data is located in the file /import/a12/users/kraemea88/two_peptides/data/allatom.h5 For an example on how to use it, see example_usage.ipynb.

TL;DR:

DATA_FILE = "/import/a12/users/kraemea88/two_peptides/data/allatom.h5"
import h5py
with h5py.File(DATA_FILE, "r") as data:
    print(data["MINI"])
    print("Available Data:", list(data["MINI"]["IL_LF"].keys()))
    print("Coordinate shape:", data["MINI"]["IL_LF"]["aa_coords"].shape)
    
    from two_peptides.h5 import string_to_topology
    print(string_to_topology(data["MINI"]["IL_LF"].attrs["topology"]))

gives

<HDF5 group "/MINI" (1213 members)>
Available Data: ['aa_coords', 'aa_forces', 'bias_energy', 'box_vectors', 'd0', 'distance', 'k', 'unbiased_energy']
Coordinate shape: (27000, 101, 3)
<mdtraj.Topology with 2 chains, 8 residues, 101 atoms, 124 bonds>

Note that access to the data directory can be very slow. It makes sense to work on a local copy of the data file instead.

Caveats

Raw simulation output is located in the subdirectory data/raw. Using this raw output directly is not recommended, as the peptide coordinates are not properly wrapped in the primary unit cell.

All minipeptides are capped.

Requirements

Mandatory:

• numpy

Optional:

• pymbar (for computing PMFs)
• openmm (for running simulations)
• click (for using the command-line interface)
• bgmol (branch two_peptides; for simulations and analysis)
• mdtraj (for simulations and analysis)
• h5py (for processing simulation output)

Simulation Settings

The simulation settings are the same as for the octapeptides, i.e.

• 9 Angstrom LJ cutoff
• 7.5-9 Angstrom LJ switching
• PME electrostatics
• amber99sbildn + TIP3P force field
• HBOND constraints
• no hydrogen mass repartitioning

Umbrella sampling was run using

• 2 fs time step
• 0.1 / ps friction constant
• a force constant of 500. kJ/mol/nm^2
• umbrella windows over the centroid bond distance from 3 to 30 Angstrom spaced in 1A intervals
• each simuation is equilibrated in NPT for 300 ps
• for each umbrella, the simulation is run for 1 ns. Coordinate/force pairs are saved every 1 ps.