Finding Force Field Parameters for Molecular Modeling | Sigma & Epsilon

In summary, the conversation discussed the use of Lennard-Jones function to calculate Van der Waals forces between atoms in molecular modeling programs. The speaker was looking for force field parameters, specifically for nonbonded interactions, and had collected various articles and links on the topic. They were particularly interested in organic compounds and had found some AMBER force field parameters available online. They requested more information on LJ parameters from the other speaker.
  • #1
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I am looking for some force field parameters for nonbonded forces between atoms.

In most molecular modeling programs Lennard-Jones function is used to calculate Van der Waals forces where sigma and epsilon are constant values for a pair of atoms. But i cannot find them anywhere.


Or if anyone has complete force field parameters (bonded and nonbonded interactions) i would be more than happy to have it!
 
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  • #2
... actually seems pretty difficult to find any online (if do some fitting etc expands a bit). What have come across & stored:

http://www3.interscience.wiley.com/cgi-bin/abstract/33880/ABSTRACT?CRETRY=1&SRETRY=0
http://arxiv.org/PS_cache/cond-mat/pdf/9805/9805048.pdf
http://www.biochemtech.uni-halle.de/PPS2/course/section7/os_non.html#lj

what atoms, solids, compounds ... , did you've in mind? I've a collection of papers about the topic where can seek some specific values.
 
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  • #3
Thank you for your links!
The last one looks the most interesting to me.
I am interested in organic compound.. so mainly C H O N P S elements.

I can't access the article on wiley page though.
 
  • #4
Weird ... I can't access that Wiley one myself anylonger :uhh: :rofl: . I can PM/email you a couple of related reports etc. about LJ parameters have collected containing those elements if you need some more specific info (something have collected along the way for a basis of own work)?
 
  • #5
Ok i found that AMBER force field parameters are avalible on their homepage: http://amber.scripps.edu/ and there is also a link to some other page where they have a nice file: http://www.chpc.utah.edu/~cheatham/cornell_all_prm

But anyway i would like more LJ parameters if you have.. see PM please.
 
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1. How do I determine the optimal values for sigma and epsilon in a force field?

The optimal values for sigma and epsilon in a force field are determined through a combination of experimental data and theoretical calculations. Experimental data such as bond lengths, angles, and energies can be used to refine the force field parameters, while theoretical calculations such as quantum mechanics simulations can provide insights into the electronic structure of the molecules and help determine appropriate values for sigma and epsilon.

2. What are the consequences of using incorrect sigma and epsilon values in molecular modeling?

Using incorrect sigma and epsilon values can result in inaccurate predictions of molecular properties and behaviors. This can lead to incorrect conclusions in research and potentially waste resources and time in drug discovery or material design. In extreme cases, incorrect force field parameters can result in unstable or unrealistic molecular structures.

3. Are there any general guidelines for selecting sigma and epsilon values in a force field?

There are no strict guidelines for selecting sigma and epsilon values as they are highly dependent on the specific molecules and systems being studied. However, it is important to consider the size, shape, and chemical properties of the molecules when selecting these parameters. It is also recommended to compare the results from multiple force fields and refine the parameters based on experimental data and theoretical calculations.

4. Can I use force field parameters from a different system for my own molecular modeling?

While it may be tempting to use force field parameters from a similar system, it is generally not recommended. Each molecule and system has its own unique characteristics and interactions, so using parameters from a different system can lead to inaccurate results. It is best to derive the parameters specifically for the system being studied.

5. How often should I update the sigma and epsilon values in my force field?

The frequency of updating sigma and epsilon values in a force field depends on the specific application and the availability of new experimental data. In general, it is recommended to periodically review and refine the parameters to ensure accurate predictions of molecular behaviors. Additionally, major updates to the force field itself may also require updates to the sigma and epsilon values.

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