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How to determine the constraint length of benzene?
- xuji_2015
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9 years 1 month ago #4502
by xuji_2015
How to determine the constraint length of benzene? was created by xuji_2015
Hi all
I want to coarse grain a molecule which contains benzene.
In MARTINI force field, the constraint length between CGs of benzene is 0.27 nm,
but I cannot get that value in my mapping scheme. Can someone help me to provide the
mapping scheme of benzene? Or explain why the constraint length is 0.27 nm?
Appreciate any help in advance!
I want to coarse grain a molecule which contains benzene.
In MARTINI force field, the constraint length between CGs of benzene is 0.27 nm,
but I cannot get that value in my mapping scheme. Can someone help me to provide the
mapping scheme of benzene? Or explain why the constraint length is 0.27 nm?
Appreciate any help in advance!
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- jaakko
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9 years 2 weeks ago - 9 years 2 weeks ago #4516
by jaakko
Replied by jaakko on topic How to determine the constraint length of benzene?
Hi,
benzene is one of those special cases where the positions of the beads are not directly based on the centers of mass. The bond length has been chosen so that the density of bulk benzene is closer to experimental data. There's a short discussion of this in the Martini paper: dx.doi.org/10.1021/jp071097f
- Jaakko
benzene is one of those special cases where the positions of the beads are not directly based on the centers of mass. The bond length has been chosen so that the density of bulk benzene is closer to experimental data. There's a short discussion of this in the Martini paper: dx.doi.org/10.1021/jp071097f
- Jaakko
Last edit: 9 years 2 weeks ago by jaakko.
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- xuji_2015
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9 years 1 week ago #4522
by xuji_2015
Replied by xuji_2015 on topic How to determine the constraint length of benzene?
Jaakko, thank you very much for your info!
But another question is how can I determine the positions of the CG beads of the benzene in the parameterizing process provided in md.chem.rug.nl/cgmartini/index.php/parametrzining-new-molecule ?
But another question is how can I determine the positions of the CG beads of the benzene in the parameterizing process provided in md.chem.rug.nl/cgmartini/index.php/parametrzining-new-molecule ?
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