Perform a simulation with an All-Atom Structure-Based Model using OpenSMOG

This tutorial should take between 5 to 15 minutes of reading and performing simulations.

Input files for this tutorial can be found here

The first step is to import the OpenSMOG module

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from OpenSMOG import SBM

SBM class sets the parameters for the simulation:

name="2ci2" Sets the name of each simulation (this name is used as prefix for the outputs). time_step=0.002 (reduced time unit) Sets the time step used in integration. collision_rate=1.0 (reduced inverse-time unit) Sets the collision rate in the Langevin integrator. r_cutoff=1.2 (nanometers) Sets the non-bonded cutoff. temperature=0.5 (reduced temperature unit) Sets the temperature for the simulation.

sbm_AA is an arbitrarily chosen variable name for the SBM object

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sbm_AA = SBM(name='2ci2', time_step=0.002, collision_rate=1.0, r_cutoff=1.2, temperature=0.5)

There are three hardware platform options to run the simulations:

platform="cuda" platform="HIP" platform="opencl" platform="cpu"

if cuda, opencl or HIP is choosen the GPUindex can be define as “0”. If two GPUs are used, one may give “0,1”

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Sets the directory name where the output files are saved

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Load the gro, top and xml files into the sbm_AA object

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sbm_AA_grofile = 'SMOG2_AA_CI2/2ci2.AA.gro'
sbm_AA_topfile = 'SMOG2_AA_CI2/'
sbm_AA_xmlfile = 'SMOG2_AA_CI2/2ci2.AA.xml'

sbm_AA.loadSystem(Grofile=sbm_AA_grofile, Topfile=sbm_AA_topfile, Xmlfile=sbm_AA_xmlfile)

This function returns the name of each contact potential that is being used in the current model. In this example, only a Lennard-Jones-style 6-12 potential is being applied.

The simulation context is created with all information given in the previous steps.

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Create the reporters that will save the simulation data in an output folder.

trajectory=True Save the trajectory in .dcd format. energies=True Save the energy in text format separated by a comma. interval=10**3 The interval (in steps) at which the trajectory and energies are saved.

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sbm_AA.createReporters(trajectory=True, energies=True, energy_components=True, interval=10**3)

The run function receives the following parameters:

nsteps=10**6 Number of steps to perform in the simulation. report=True Shows the simulation details (Progress (%), Step and Time Remaining) interval=10**3 The step interval to show the details

[ ]:**6, report=True, interval=10**3)

The output files are located in the output folder