First example

This section provides a simple example to illustrate how to use VLMP. The example demonstrates how to simulate a set of DNA chains using the MADna model. We begin by setting various simulation parameters such as the number of sequences, sequence length, and others. The script then generates random DNA sequences and populates the simulation pool with the necessary configuration. Finally, VLMP is initialized, and the simulation pool is loaded and distributed.

import VLMP
from VLMP.utils.units import picosecond2KcalMol_A_time
from numpy import random

# Convert picoseconds to AKMA time unit
ps2AKMA = picosecond2KcalMol_A_time()

# Number of sequences and sequence set size
Nsequence = 10
sequenceSetSize = 10

# Length of each sequence and the basis of DNA
sequenceLength  = 100
basis = ['A', 'C', 'G', 'T']

# Generate random sequences
sequences = []
for i in range(Nsequence):
    sequences.append(''.join(random.choice(basis, sequenceLength)))

# Populate simulation pool
simulationPool = []
for seq in sequences:
    # Configure simulation parameters
    simulationPool.append({
        "system": [
            {"type": "simulationName", "parameters": {"simulationName": seq}},
            {"type": "backup", "parameters": {"backupIntervalStep": 100000}}
        ],
        "units": [{"type": "KcalMol_A"}],
        "types": [{"type": "basic"}],
        "ensemble": [
            {"type": "NVT", "parameters": {"box": [2000.0, 2000.0, 2000.0],
                                           "temperature": 300.0}}
        ],
        "integrators": [
            {"type": "BBK", "parameters": {"timeStep": 0.02*ps2AKMA,
                                           "frictionConstant": 0.2/ps2AKMA,
                                           "integrationSteps": 1000000}}
        ],
        "models": [
            {"type": "MADna", "parameters": {"sequence": seq}}
        ],
        "simulationSteps": [
            {"type": "saveState", "parameters": {"intervalStep": 10000,
                                                 "outputFilePath": "traj",
                                                 "outputFormat": "dcd"}},
            {"type": "thermodynamicMeasurement", "parameters": {"intervalStep": 10000,
                                                                "outputFilePath": "thermo.dat"}},
            {"type": "info", "parameters": {"intervalStep": 10000}}
        ]
    })

# Initialize VLMP and load simulation pool
vlmp = VLMP.VLMP()
vlmp.loadSimulationPool(simulationPool)

# Distribute simulations and set up
vlmp.distributeSimulationPool("size", sequenceSetSize)
vlmp.setUpSimulation("FIRST_EXAMPLE")

Executing Simulations

To execute the simulations, use the following terminal command:

python -m VLMP -s VLMPsession.json --local --gpu 0 1

Run this command in the directory “FIRST_EXAMPLE,” which is created by the preceding code. The –local flag indicates that the simulations will run on the current machine. However, VLMP provides the option to run simulations on other machines like a HPC cluster. The –gpu 0 1 option specifies that GPUs 0 and 1 will be used for the simulations.