Simple water potential for MD Simulation

In summary, the person is looking for a model to use in a molecular dynamics simulation with atoms in water. They mention using a one-site model with a Lennard-Jones potential, but are open to other suggestions. They also mention the possibility of simulating a smaller system and considering the effects of water, such as polarization. They suggest checking out standard MD software for potential options.
  • #1
Boltzfan
1
0
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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  • #2
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.
 

1. What is simple water potential in MD simulation?

Simple water potential is a mathematical function that describes the energy interactions between water molecules in a molecular dynamics (MD) simulation. It takes into account the attractive and repulsive forces between water molecules, as well as the interactions with the surrounding environment.

2. How is simple water potential calculated in MD simulation?

Simple water potential is typically calculated using a force field, which is a set of mathematical equations and parameters that describe the energy interactions between water molecules. These equations take into account the distance between water molecules, as well as their charges and polarizabilities.

3. What factors influence simple water potential in MD simulation?

The factors that influence simple water potential in MD simulation include the geometry and arrangement of water molecules, the temperature and pressure of the system, and the type of force field used. Other factors such as ions or other solutes in the water can also affect the water potential.

4. How does simple water potential affect the behavior of water molecules in MD simulation?

Simple water potential determines the energy interactions between water molecules, which in turn affects their movement, arrangement, and dynamics in the simulation. It can also influence the properties of water, such as its density and viscosity.

5. What are the limitations of using simple water potential in MD simulation?

Simple water potential is based on simplified mathematical models and may not accurately capture all the complexities of real water molecules. It also relies on the choice of force field, which may not be suitable for all systems. Additionally, it does not take into account quantum effects that may be important in certain situations.

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