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Building a star CG polymer?
- xudongh
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11 years 5 months ago #1263
by xudongh
Building a star CG polymer? was created by xudongh
Hello all. I am a new undergraduate student who just joined a research project.
I am trying to build a CG model of the following polymer: english.cast.org.cn/n1181872/n1182068/n12716933/14115597.html [in essence it's a star copolymer with a core and multi arm connected to the core. ]
How would I go about approaching to build such polymer and apply coarse graining to it and eventually simulate it in gromacs?
My theory is I have to create the structure in ChemDraw and then make it into PDB and then start the gromacs work from there?
Or do I have to perform self assembly in gromacs?
Any help is appreciated. Thank you.
I am trying to build a CG model of the following polymer: english.cast.org.cn/n1181872/n1182068/n12716933/14115597.html [in essence it's a star copolymer with a core and multi arm connected to the core. ]
How would I go about approaching to build such polymer and apply coarse graining to it and eventually simulate it in gromacs?
My theory is I have to create the structure in ChemDraw and then make it into PDB and then start the gromacs work from there?
Or do I have to perform self assembly in gromacs?
Any help is appreciated. Thank you.
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- djurre
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11 years 5 months ago #1268
by djurre
Replied by djurre on topic Building a star CG polymer?
First you will need a topology, eg parameters that determine how the molecule will behave (a .top/.itp file). The molecule might be similar (or the same) as the PAMAM dendrimers parametrized by Lee et al. (Lee H, Larson RG, J. Phys. Chem. B 112, 7778-7784, 2008). Have a look at that article how they did it. The parameters you can find here:
cgmartini.nl/index.php/peg/105-polymers
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