Molecular Dynamics Simulation - How Do You Find Parameters?

[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!

 

[Useful nucleus]

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

 

[engineering lord]

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.

 

[Useful nucleus]

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/