Parametrizing a new molecule based on known fragments

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4 years 5 months ago #8326 by Hot

Parametrizing a new molecule based on known fragments was created by Hot

I'm parameterizing a new molecule. All fragments of the new molecule can be divided into known beads, that is to say, all parameters such as bond length and angle can be found from the previous molecules. In this case, do I need to optimize the CG bonded parameters by comparing the bond distribution of all atoms and CG.

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bart
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4 years 5 months ago #8327 by bart

Replied by bart on topic Parametrizing a new molecule based on known fragments

In the end you have to convince yourself and others that your CG model is fit for the purpose you use it for. Verifying bonded parameters is the standard, if you have another option that is fine. Dihedrals tend to be very molecule dependent, bonds and angles can (sometimes) be inherited.

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4 years 5 months ago #8328 by Hot

Replied by Hot on topic Parametrizing a new molecule based on known fragments

If I directly use the parameters of the existing molecules to run the CG simulation without all atom simulation, the obtained density and other parameters are not much different from the experimental values, is this result credible?

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4 years 5 months ago #8329 by bart

Replied by bart on topic Parametrizing a new molecule based on known fragments

I really cant make that decision for you without knowing the ins and outs of what you want to do. This is were you as a scientist have to be critical to your own work.

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4 years 5 months ago #8330 by Hot

Replied by Hot on topic Parametrizing a new molecule based on known fragments

Yeah, you are right. Attitude is important.
I am now building a model of polyester. And I am following the tutorial to extract the parameters of the all-atom. I just want to know if the process of all-atom simulation parameters is necessary, because all the parameters can be found from the previous molecules.

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bart
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4 years 5 months ago #8331 by bart

Replied by bart on topic Parametrizing a new molecule based on known fragments

I am not very knowledgeable with respect to polymers so I would not dare to say, maybe someone working on polymers can answer this question.

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Parametrizing a new molecule based on known fragments