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Polymer Radius of gyration
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7 years 9 months ago #5741
by ywang52
Polymer Radius of gyration was created by ywang52
Hi guys,
I am very new here. I am trying to use Martini to simulate an amphiphilic polymer. I just calculated the radius of gyration of the whole molecule, the back bone, and the Rg of the hydrophobic chain and the hydrophilic chain in each repeat unit. The Rg of the whole molecule and the Rg of the backbone is pretty close to the value obtained from the atomistic simulation according to the literature. However, the Rg of the small hydrophilic and hydrophobic chain is much smaller than the atomistic value (somehow close to the quarter of the value). I am wondering if it is because of the 4:1 mapping. Since I draw the molecule by Avogadro, those CG beads are actually represented by normal atoms, I guess the size of each beads is actually about a quarter of its actual value? Also, the polymer includes 40 repeat unit, so I guess the Rg of the whole polymer is not affected much by the size of each single bead, and therefore the Rg of the whole polymer is close to the actual value from the atomistic simulation?
I am very new here. I am trying to use Martini to simulate an amphiphilic polymer. I just calculated the radius of gyration of the whole molecule, the back bone, and the Rg of the hydrophobic chain and the hydrophilic chain in each repeat unit. The Rg of the whole molecule and the Rg of the backbone is pretty close to the value obtained from the atomistic simulation according to the literature. However, the Rg of the small hydrophilic and hydrophobic chain is much smaller than the atomistic value (somehow close to the quarter of the value). I am wondering if it is because of the 4:1 mapping. Since I draw the molecule by Avogadro, those CG beads are actually represented by normal atoms, I guess the size of each beads is actually about a quarter of its actual value? Also, the polymer includes 40 repeat unit, so I guess the Rg of the whole polymer is not affected much by the size of each single bead, and therefore the Rg of the whole polymer is close to the actual value from the atomistic simulation?
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7 years 9 months ago #5743
by ywang52
Replied by ywang52 on topic Polymer Radius of gyration
Hi, all. That was a dumb question, I made some mistake, and now I have figured it out. Please just ignore it.
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