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Intramolecular Coulombic interactions
- bernardR
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8 years 5 months ago #5017
by bernardR
Intramolecular Coulombic interactions was created by bernardR
Hello,
I have a question regarding electrostatic interactions inside molecules. It is clear from the Marrink et al. 2007 paper that LJ interactions between second nearest neighbors have to be included, but what about electrostatics?
Do I have to consider electrostatic interactions between charged beads in the same molecule? Between first, second, or farther neighbors?
Thanks in advance,
Bernard
I have a question regarding electrostatic interactions inside molecules. It is clear from the Marrink et al. 2007 paper that LJ interactions between second nearest neighbors have to be included, but what about electrostatics?
Do I have to consider electrostatic interactions between charged beads in the same molecule? Between first, second, or farther neighbors?
Thanks in advance,
Bernard
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- mnmelo
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8 years 5 months ago #5042
by mnmelo
Replied by mnmelo on topic Intramolecular Coulombic interactions
Hi Bernard,
In that regard electrostatics are treated just like LJ interactions are. Non-first neighbors interact with normal Martini electrostatics (shifted coulomb potential between 0.0 and 1.2nm, with a dielectric constant of 15).
This isn't a hard rule, however. You'll find that molecules with tight mappings and stiff bonded interactions -- cholesterol, for instance -- exclude more than just first neighbors from nonbonded interactions.
In the end you'll want your topology to properly recreate intramolecular distance distributions. Excluding nonbonded interactions between more than first neighbors, or even between arbitrary pairs of beads, is just another of many resources to achieve that goal.
Cheers,
Manel
In that regard electrostatics are treated just like LJ interactions are. Non-first neighbors interact with normal Martini electrostatics (shifted coulomb potential between 0.0 and 1.2nm, with a dielectric constant of 15).
This isn't a hard rule, however. You'll find that molecules with tight mappings and stiff bonded interactions -- cholesterol, for instance -- exclude more than just first neighbors from nonbonded interactions.
In the end you'll want your topology to properly recreate intramolecular distance distributions. Excluding nonbonded interactions between more than first neighbors, or even between arbitrary pairs of beads, is just another of many resources to achieve that goal.
Cheers,
Manel
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- bernardR
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8 years 5 months ago #5043
by bernardR
Replied by bernardR on topic Intramolecular Coulombic interactions
Hi Manel,
Thank you very much for your reply. Do you have any reference paper where this is explicitly written?
Best regards,
Bernard
Thank you very much for your reply. Do you have any reference paper where this is explicitly written?
Best regards,
Bernard
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- mnmelo
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8 years 5 months ago #5044
by mnmelo
Replied by mnmelo on topic Intramolecular Coulombic interactions
The overall attitude is described in the J Phys Chem 2007 paper. The particular case of cholesterol is also explained there -- though, as you noted, emphasis was put on the LJ exclusions but not the Coulombic ones.
But I doubt you'll find a paper with all these instructions clearly written down. On the other hand, the growing literature on Martini molecule parameterization neatly showcases several different possible approaches.
Cheers,
Manel
But I doubt you'll find a paper with all these instructions clearly written down. On the other hand, the growing literature on Martini molecule parameterization neatly showcases several different possible approaches.
Cheers,
Manel
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