A question about how to start ab initio simulations

In summary, the conversation discusses the best approach for simulating STM images of a compound composed of 3 molecules A, B, and C. The two options considered are using the known equilibrium geometries of A, B, and C as input, or optimizing their geometries independently before simulating the compound. The speaker has tried both methods and found slight differences in the resulting structures. They are also considering the accuracy of the experimental geometries and the effect of different methods on the optimization results. In general, the speaker takes the experimentally confirmed equilibrium geometry and optimizes it with their program, using a different method if necessary.
  • #1
ftft
21
0
I want to simulate STM images of some compound composed of 3 molecules A, B and C..
Which is the right way to do the simulations?
*Use the known equilibrium geometries of A, B and C as input for simulating the compound? or
*First optimize the geometries of A, B and C independently and then use their optimized geometries in simulating the compound
I have tried both ways and there were tiny differences in the resulting compound structures.. Still, I need to check for academic accuracy..

Thanks in advance
 
  • #3
What do you mean "known" equilibrium geometries? Were those found by other peoples' simulations? Was it through experiment? What is the chance the experimental geometries are a little off due to the experimental method used?
When doing the ab initio optimizations of A, B, and C, did different methods, basis sets, functionals produce different results?

Those are some questions to think about. As for me, I generally take the experimentally confirmed equilibrium geometry, optimize it with my program, and if I get worryingly different results, I try a different method for the optimization.
 

Related to A question about how to start ab initio simulations

1. What is the meaning of "ab initio" in scientific simulations?

"Ab initio" is a Latin term meaning "from the beginning" or "from first principles". In scientific simulations, it refers to the method of starting from the fundamental laws and equations of a system and using them to make predictions without any prior assumptions or experimental data.

2. What types of systems can be studied using ab initio simulations?

Ab initio simulations can be used to study a wide range of systems, including atoms, molecules, materials, and biological systems. They are particularly useful for studying systems at the atomic and molecular level, where classical methods may not be accurate enough.

3. How do you set up an ab initio simulation?

An ab initio simulation involves several steps, including setting up the initial system, choosing the appropriate computational method, and optimizing the parameters. The system is then simulated using numerical algorithms, and the results are analyzed to make predictions about the behavior of the system.

4. What are the advantages of using ab initio simulations?

Ab initio simulations have several advantages over other methods, including the ability to study systems without prior experimental data, high accuracy, and the ability to model complex systems. They also allow for the study of systems at various length and time scales, making them versatile tools for scientific research.

5. Are there any limitations to ab initio simulations?

While ab initio simulations have many advantages, they also have limitations. They can be computationally expensive and may not be suitable for studying large systems or long time scales. They also rely on the accuracy of the underlying equations and may not be applicable to all systems. Additionally, the interpretation of results can be challenging and requires a thorough understanding of the methods used.

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