We've learned how to generate a MD simulation structure after polymer modeling on the previous module tip: How to perform the polymer simulation – Polymer MD Modeling.
MD simulations can be performed to obtain several properties of materials using the prepared structures. However, it is not recommended to run simulations to obtain properties using the initial structure. In order to obtain accurate properties, it is necessary to sufficiently stabilize the initial structure under the calculation conditions.
Generally, thermal equilibrium at a particular temperature is considered to be the proper state for the system to obtain physical or chemical properties. The process by which an object reaches thermal equilibrium, 'Thermalization', can be described as a structural optimization process.
This process can be performed in the 'LAMMPS (Thermalization)' module.
In this module tip, we will explain the 'Thermalization' module that must be performed before obtaining the physical or chemical properties of polymer using MD simulation.
1. Prepare MD Model
First, you need to prepare the MD model to perform 'Thermalization' calculation.
The process of structural modeling can be found in the previous post: How to perform the polymer simulation? – Polymer MD Modeling.
2. Perform Thermalization Calculation
Add the 'LAMMPS (Thermalization)' module. Then set the initial parameters and start the job.
You can run the simulation without difficulty by adjusting the 'Temperature' and 'Density' in general among the several parameters in the 'LAMMPS (Thermalization)' module.
'Temperature' parameter is the temperature at which thermal stabilization will be performed, and it is recommended to set it according to the starting temperature in the property simulation that will be connected later. 'Density' parameter is the density that the system ultimately has.
When you submit a 'LAMMPS (Thermalization)' job, the NVT simulation runs continuously until the set the 'Target Density' is reached while reducing the cell volume. This method is essentially the same as NPT, except that, unlike when the NPT option is selected, equilibrium is achieved for each volume before proceeding to the next step. For these reasons, the progress of the NVT simulation is more stable than NPT, which is especially advantageous for creating dense polymer models.
After the calculation is finished, you can check the result on the 'Analysis' tab.
First, when you play the Trajectory movie, you can see the changes in the system in the form of animation. Changes in system temperature, volume, and energy can also be checked in the graph.
If the problem still occurs when optimizing, you should check the following:
1. Did you choose the 'Dreiding' potential?
2. Is the target 'Density' set to an appropriate value?
If there are no errors in the above settings (Potential or/and Density) and you are still having problems, please turn off 'Coulombic interaction' or lower 'time step' in the 'Advanced Options' to less than 0.5fs and perform the calculations. It is also advisable to set the cell parameters to large values to reduce the initial density during modeling.
In this module tip, we learned how to achieve the thermal equilibrium of the polymer system in terms of molecular dynamics using the 'LAMMPS (Thermalization)' module.
In the next module tip, we'll explain how to calculate useful properties from a polymer system that has achieved thermal equilibrium.
Thank you very much for your attention.
🍀Need more information?
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LAMMPS : Molecular Dynamics Simulation for Polymer – Polymer MD
LAMMPS : How to perform the polymer simulation – Polymer MD Modeling