Molecular Dynamics Simulation - How Do You Find Parameters?

In summary, the conversation discusses the use of molecular dynamics simulation programs like Lammps and Amber for material science research. The individual is seeking advice on finding accurate parameters for their simulations and is directed to consult with their research advisor and conduct a literature review. They are also recommended to try simulating a Lennard-Jones system and read "Understanding molecular simulation" by D. Frenkel and B. Smit. Additional resources, such as video lectures from an MIT course, are also suggested.
  • #1
engineering lord
Hi all,
I'm doing a bit of material science research at my university. I'm running molecular dynamics simulation programs like Lammps and Amber as part of it, and I'm pretty new to the whole thing (just like I'm pretty new to this forum). I'd like to ask, has anyone here used Amber to find their bond, angle, and dihedral coefficients to use in Sander or Lammps? I'm having a lot of trouble finding accurate parameters to run for my simulations, and I need some advice from someone who has done it before.
Thank you!
 
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  • #2
There is no general recipe to share. Choosing simulation parameters is typically done by careful literature review and consultation with your research advisor. If you have a specific question on certain material/system and/or force field, feel free to post it and I will try to help if I'm familiar with it.

As a starter and if you want to gain experience on a simple system, try to simulate a Lennard-Jones system. This is straightforward. Some reading in the text "Understanding molecular simulation" by D. Frenkel and B. Smit can also be very helpful
 
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  • #3
Useful nucleus said:
There is no general recipe to share. Choosing simulation parameters is typically done by careful literature review and consultation with your research advisor. If you have a specific question on certain material/system and/or force field, feel free to post it and I will try to help if I'm familiar with it.

As a starter and if you want to gain experience on a simple system, try to simulate a Lennard-Jones system. This is straightforward. Some reading in the text "Understanding molecular simulation" by D. Frenkel and B. Smit can also be very helpful
Thank you so much for pointing me in the right direction! I am requesting that book right now from my university library.
 
  • #4
Also if you prefer to watch some video lectures first, then lectures 1, 2 and 13,14 in this MIT course should give you a great idea about molecular dynamics and force fields.
https://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/video-lectures/
 
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1. What is molecular dynamics simulation?

Molecular dynamics simulation is a computational technique used to study the behavior of atoms and molecules over time. It involves solving the equations of motion for each atom in a system, taking into account the interatomic forces and interactions, to simulate the movement and interactions of the particles.

2. Why is it important to find parameters in molecular dynamics simulation?

Finding accurate and reliable parameters is crucial in molecular dynamics simulation because it directly affects the accuracy and validity of the simulation results. The parameters determine the forces and interactions between particles, and therefore, incorrect parameters can lead to erroneous conclusions.

3. How do you find parameters for molecular dynamics simulation?

There are various methods for finding parameters in molecular dynamics simulation, including force field-based methods, ab initio calculations, and experimental data. Force field-based methods involve using mathematical functions to describe the interactions between particles, while ab initio calculations use quantum mechanical principles to determine the parameters. Experimental data, such as bond lengths and angles, can also be used to determine parameters.

4. What are some challenges in finding parameters for molecular dynamics simulation?

One of the main challenges in finding parameters for molecular dynamics simulation is the lack of experimental data for certain systems. This can make it difficult to accurately determine the parameters, and in some cases, force field-based methods may need to be used instead. Additionally, the accuracy and reliability of the parameters can also be affected by the choice of force field and the level of theory used in ab initio calculations.

5. Are there any limitations to using molecular dynamics simulation for parameter determination?

While molecular dynamics simulation is a powerful tool for studying the behavior of atoms and molecules, it is not without limitations. One of the main limitations is the computational cost, as simulations can require significant computing resources and time. Additionally, the accuracy of the simulation results is highly dependent on the quality of the parameters used, which can be challenging to determine accurately.

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