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MARTINI dihedral for a organic molecule
- satti
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9 years 2 weeks ago #4508
by satti
MARTINI dihedral for a organic molecule was created by satti
Dear all,
I am trying to make a martini itp for a molecule. A part of the molecule could be described as a flexible substituent on a benzene ring (C6H5)-C1-C2-(NH3)+. Comparing the mapping of Glutamine and Lysine, both with 5 heavy atoms in their sidechains, I find that Gln sidechain is made of 1 bead while Lys sidechain has 2 beads. For now I settled on giving a try with three SC4 particle as in Benzene, with one of three SC4 particles would be mapped to three C atoms of ring plus C1, and a Qd particle for C1-C2-(NH3)+. Is this mapping OK?
I have done some some test simulations. The AT simulations, when mapped as above shows that the dihedral Qd-SC4-SC4-SC4, show a bimodal distribution at +/- 15 degree. When I did the CG simulations, I find the same dihedral to be unimodal around 0 degrees. Any suggestions how can I correct for this, if possible.
with best regards,
satti
I am trying to make a martini itp for a molecule. A part of the molecule could be described as a flexible substituent on a benzene ring (C6H5)-C1-C2-(NH3)+. Comparing the mapping of Glutamine and Lysine, both with 5 heavy atoms in their sidechains, I find that Gln sidechain is made of 1 bead while Lys sidechain has 2 beads. For now I settled on giving a try with three SC4 particle as in Benzene, with one of three SC4 particles would be mapped to three C atoms of ring plus C1, and a Qd particle for C1-C2-(NH3)+. Is this mapping OK?
I have done some some test simulations. The AT simulations, when mapped as above shows that the dihedral Qd-SC4-SC4-SC4, show a bimodal distribution at +/- 15 degree. When I did the CG simulations, I find the same dihedral to be unimodal around 0 degrees. Any suggestions how can I correct for this, if possible.
with best regards,
satti
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- jaakko
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9 years 1 week ago #4517
by jaakko
Replied by jaakko on topic MARTINI dihedral for a organic molecule
Hi,
The mapping sounds reasonable but testing will tell you that better. If you want to fix the dihedral you could try using a Ryckaert-Bellemans type dihedral there that allows modeling such bimodal distributions ( http://www.gromacs.org/Documentation/Terminology/Dihedral )
- Jaakko
The mapping sounds reasonable but testing will tell you that better. If you want to fix the dihedral you could try using a Ryckaert-Bellemans type dihedral there that allows modeling such bimodal distributions ( http://www.gromacs.org/Documentation/Terminology/Dihedral )
- Jaakko
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