Simple water potential for MD Simulation

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SUMMARY

The discussion centers on optimizing molecular dynamics (MD) simulations involving water, specifically addressing the challenges of simulating water in a vacuum. A one-site model using Lennard-Jones potential is suggested, but the importance of considering water's polarization is emphasized. Participants recommend simulating smaller systems for better reliability and suggest incorporating electric dipoles into water models. Additionally, they advise evaluating the necessity of water in the simulation to ensure meaningful results.

PREREQUISITES
  • Understanding of molecular dynamics simulations
  • Familiarity with Lennard-Jones potential
  • Knowledge of water's polarization effects
  • Experience with MD simulation software
NEXT STEPS
  • Research methods for simulating coarse-grained water models
  • Learn about incorporating electric dipoles in MD simulations
  • Explore standard MD software options for water simulations
  • Investigate the impact of system size on simulation accuracy
USEFUL FOR

Researchers and practitioners in computational chemistry, molecular dynamics specialists, and anyone involved in simulating aqueous environments in MD simulations.

Boltzfan
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Hi. I have to do a molecular dynamics simulation with atoms in water. The simulation takes a lot of time in vacuum so I can't have a very sophisticated model (like 3 body collisions) for water. I was thinking of a one-site model with a Lennard-Jones potential, but I was wondering if there was not another model that could be used without taking a lot of time to calculate.

Thank you for answers and suggestions.
 
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Since you didn't get a reply so far, a few random remarks of mine:
- You're very vague with "an MD simulation with atoms in water". There is a huge amount of possibilities for you. The most obvious one, although not directly answering your question, is simulating a smaller system. That may sound disappointing, but from my experience you're often better off with a smaller system that you can simulate properly rather than a larger system whose results you cannot really trust because sanity checks would take too long to perform.
- I'm not a super expert on MD simulations of ?, but the first thing that comes to my mind when thinking about simulating water is its polarization that the LJ fluid doesn't have - I'd at least add an electric dipole to your water beads if you need it.
- Another question you should ask yourself is: why do you want water in your system? If you only want it because your system is in water in reality, but you don't expect the water to have any effect then you should he honest about this point and throw out the water altogether rather than adding something to your simulation and pretending it is water.
- There is a lot of standard MD software available. You may check them out whether they are an option for you, or maybe just how they simulate coarse grained water.
 

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