The Basics of Molecular Simulations: Part-3
This is a 3-part series on the basics of molecular simulations.
In Part-1, I talked about the fundamental idea behind molecular simulations and its applications in the field of material science and drug discovery in brief. I explained how ensembles are defined to mimic the experimental conditions to conduct molecular simulations. Furthermore, I described Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) simulation techniques with used case scenarios.
In Part-2, I discussed the system definition and input forcefield parameters needed to carry out these simulations. I talked about the Crystallographic Information File (CIF), atomic charges, non-bonded, and bonded forcefield parameters with examples. For those, who didn’t check the Part-1 and 2, please read it before going further.
In Part-3, I will explain the tools and software, I have used to perform molecular simulations. Please note that I have used molecular simulations for materials, so I will talk about it from that perspective.
Pre-Simulations
In this step, we prepare the file which has the geometrical setup information of the structure.
CIF File:
You can refer to the repository below to find the CIF file for the material, you want to study. It has many CIF files.
The Cambridge Structural Database (CSD) database also has over one million structures.
Tip: CIF files are obtained from experiments. If you can’t find the structure in the online database, try to find the experimental papers in which your material has been studied. Sometimes, the authors provide the CIF file with the supporting information. If not, you can ask them directly.
CIF2Cell:
Most software don’t directly take the CIF file as an input. We need to convert them to a different format based on the software; we are using. For e.g., LAMMPS has its own input file format called “data file”.
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF file. People write their own code to convert the CIF file to the desired format. But, if you don’t want to do that, you can directly use this tool to generate the required file type. Check below for more details,
Running Simulations
Now, in this step, we choose the software based on our requirements.
RASPA:
It is mostly used to perform GCMC simulations to study the equilibrium properties of the systems such as vapor-liquid equilibrium, adsorption properties, and more. It is the most convenient software to perform GCMC and super easy to use. I used it to calculate material adsorption properties and some others such as surface area, void fraction, and pore-size distribution. RASPA can also do charge equilibration (Qeq) to get the charges on metal atoms very fast which I discussed in Part-2. To know more about other features, refer to the paper below,
The only problem is that RAPSA is a serial code not parallel, so it might not be suitable for systems that are large in size. For e.g., I tried to perform GCMC for MIL-101, it didn’t work out very well.
LAMMPS:
LAMMPS is the most used software to perform MD simulations to study materials. It is open software and has parallel computing. It has a range of features, methods, algorithms, and more. By using LAMMPS, you can get an actual feel of the physics and dynamics of the system.
There are other softwares which have GUI, you just provide the parameters and run. But you won’t have the flexibility to play around the physics that much.
Post Simulations
Here, you do the post-processing of the MD simulations results.
VMD (Visual molecular dynamics):
VMD is used to analyze the trajectory of the system you have performed the MD simulations. It supports a variety of file types. The most common one is the PDB file. You get the results of MD simulations in the form of an output PDB file. VMD is then used to visualize it.
VESTA:
VETSA is a very powerful tool to analyze the crystal structures. It can provide you high-quality images for publications. For e.g.
It can properly identify the linkages between atoms. In my system, I had some CO2 atoms. It was able to recognize them separately. While the other software was mixing up the CO2 atoms with the MOF atoms and forming the wrong structure.
Also, it can provide other information about the structure like PXRD patterns. It can help when we want to validate experimental results with that of simulations. In my case, I had the PXRD pattern from the experiment which was then compared with that of simulations to verify the structure.
This is the end of 3 part series covering the molecular simulations (theory, input parameters, and tools to run them). In the future, I will cover how to use RASPA and LAMMPS.
Thank you for reading. We researchers, acquire a lot of knowledge pertaining to our research. Hence, I have taken an initiative to pass on the knowledge to fellow researchers. This would save a lot of time for them which would be very valuable for their research. If you want to be a part of this initiative and wish to do the same, contact me at aankit.agrawal1995@gmail.com.
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