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Coronene MARTINI parametrization
- Bernabei
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9 years 4 months ago #4216
by Bernabei
Coronene MARTINI parametrization was created by Bernabei
Hello everybody!
My name is Marco from the university Autonoma in Madrid.
I am quite new with MARTINI and I am trying to parametrize the coronene molecule (ak superbenzene)
en.wikipedia.org/wiki/Coronene
I cannot find a way to combine the Martini's CG bead in such a way to preserve the symmetry of the molecule.
Once obtained the parametrization we would like to test the solubility in heptane and toluene.
I hope you can help me, although I have the feeling that in order to simulate coronene-like molecule we should use something like OPSL-AA(UA) or similar.
All the best!
Marco
My name is Marco from the university Autonoma in Madrid.
I am quite new with MARTINI and I am trying to parametrize the coronene molecule (ak superbenzene)
en.wikipedia.org/wiki/Coronene
I cannot find a way to combine the Martini's CG bead in such a way to preserve the symmetry of the molecule.
Once obtained the parametrization we would like to test the solubility in heptane and toluene.
I hope you can help me, although I have the feeling that in order to simulate coronene-like molecule we should use something like OPSL-AA(UA) or similar.
All the best!
Marco
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- mnmelo
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9 years 4 months ago #4219
by mnmelo
Replied by mnmelo on topic Coronene MARTINI parametrization
Hi Marco,
I thought about your superbenzene and came up with a mapping that preserves all its 6 symmetry axis (if I counted correctly).
Please appreciate below a piece of ASCII art representing coronene. I suggest a 2-to-1 mapping (just like regular benzene), where the atoms involved are those over the bonds I mark in red. I'd recommend using the SC5 bead typed defined in martini 2.2.
The center of the molecule gets maybe a bit low bead density, but not enough for other molecules to tunnel through.
To keep such a thing planar consider using virtual sites based on a triangular constraint frame.
Let me know how it goes,
Manuel
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_/ \_
/ \_/ \
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/ \_/ \
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\_/
I thought about your superbenzene and came up with a mapping that preserves all its 6 symmetry axis (if I counted correctly).
Please appreciate below a piece of ASCII art representing coronene. I suggest a 2-to-1 mapping (just like regular benzene), where the atoms involved are those over the bonds I mark in red. I'd recommend using the SC5 bead typed defined in martini 2.2.
The center of the molecule gets maybe a bit low bead density, but not enough for other molecules to tunnel through.
To keep such a thing planar consider using virtual sites based on a triangular constraint frame.
Let me know how it goes,
Manuel
_
_/ \_
/ \_/ \
\_/ \_/
/ \_/ \
\_/ \_/
\_/
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- Bernabei
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9 years 4 months ago #4220
by Bernabei
Replied by Bernabei on topic Coronene MARTINI parametrization
Dear Manuel,
Thank you very much for your input.
I had thought about this configuration, I just was not fully convinced about leaving the density hole in the middle.
Do you think that a representation with 13 beads on a triangular lattice, namely putting one in the middle with respect to your suggestion, would make any sense?
Also I was thinking about using SC4 (like benzene) for the outer beads and beads with less polar affinity (SC1 maybe?) for the inner ones.
Thank you,
all the best
Marco
Thank you very much for your input.
I had thought about this configuration, I just was not fully convinced about leaving the density hole in the middle.
Do you think that a representation with 13 beads on a triangular lattice, namely putting one in the middle with respect to your suggestion, would make any sense?
Also I was thinking about using SC4 (like benzene) for the outer beads and beads with less polar affinity (SC1 maybe?) for the inner ones.
Thank you,
all the best
Marco
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9 years 4 months ago #4236
by mnmelo
Replied by mnmelo on topic Coronene MARTINI parametrization
Hi again,
The hole in the middle shouldn't be problematic, and, after all, we're taking about a coarse grain model. I wouldn't try to add more beads unless I was sure the uneven density causes problems with interactions.
I also see no reason to have beads of different polarity. Unless somehow coronene has more polarizable edges. In any case, the SC5 beads are the ones you should use (see the most recent solvent.itp of benzene, there's a note there why the bead type was changed).
Cheers and good luck,
Manuel
The hole in the middle shouldn't be problematic, and, after all, we're taking about a coarse grain model. I wouldn't try to add more beads unless I was sure the uneven density causes problems with interactions.
I also see no reason to have beads of different polarity. Unless somehow coronene has more polarizable edges. In any case, the SC5 beads are the ones you should use (see the most recent solvent.itp of benzene, there's a note there why the bead type was changed).
Cheers and good luck,
Manuel
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- Bernabei
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9 years 4 months ago #4238
by Bernabei
Replied by Bernabei on topic Coronene MARTINI parametrization
Thank you very much Manuel,
I have already performed some Umbrella Sampling (with GROMACS) calculation of coronene in heptane at T=300K and P=1atm.
in order to get the PMF between the center of masses. The dimerization energy, estimated like the difference between the PFM a large distances and the minimum of the PMF, is of the order of 50 KJ/mol.
This results strikes with recent foundings for the PMF of coronene-like molecules, modeled with OPLS-AA, which is of the order of 10KJ/mol, (such molecules are model for asphaltenes, and basically the are like coronene decorated with an extra aromatic ring and 3 aliphatic rings, in total 35 carbons, against the 24 of the coronene).
I am running new simulations changing the crossed terms SC5-C1(heptane/octane) to get a PFM of the same order of magnitude of atomistic simulations. What do you think?
Thanks,
all the best
Marco
I have already performed some Umbrella Sampling (with GROMACS) calculation of coronene in heptane at T=300K and P=1atm.
in order to get the PMF between the center of masses. The dimerization energy, estimated like the difference between the PFM a large distances and the minimum of the PMF, is of the order of 50 KJ/mol.
This results strikes with recent foundings for the PMF of coronene-like molecules, modeled with OPLS-AA, which is of the order of 10KJ/mol, (such molecules are model for asphaltenes, and basically the are like coronene decorated with an extra aromatic ring and 3 aliphatic rings, in total 35 carbons, against the 24 of the coronene).
I am running new simulations changing the crossed terms SC5-C1(heptane/octane) to get a PFM of the same order of magnitude of atomistic simulations. What do you think?
Thanks,
all the best
Marco
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9 years 4 months ago #4240
by mnmelo
Replied by mnmelo on topic Coronene MARTINI parametrization
Hi Marco,
I'd be very careful when tweaking the interaction between bead types. If you do that blindly you might end up with a topology largely incompatible with the rest of the Martini world (how much that is a problem is up to you and what you'll use your topology with).
That said, you should aim at recovering the partition/binding energies you expect for the systems you'll study, and in that sense you approach seems ok. The 'careful' part I mentioned earlier comes when you add more components of your system and it'll be up to you to show that the interactions between coronene, those new components, and hexadecane all respect their relative preferences.
Cheers,
Manel
I'd be very careful when tweaking the interaction between bead types. If you do that blindly you might end up with a topology largely incompatible with the rest of the Martini world (how much that is a problem is up to you and what you'll use your topology with).
That said, you should aim at recovering the partition/binding energies you expect for the systems you'll study, and in that sense you approach seems ok. The 'careful' part I mentioned earlier comes when you add more components of your system and it'll be up to you to show that the interactions between coronene, those new components, and hexadecane all respect their relative preferences.
Cheers,
Manel
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- Bernabei
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9 years 4 months ago #4263
by Bernabei
Replied by Bernabei on topic Coronene MARTINI parametrization
Hi Manuel,
thanks for your answer.
I 'll keep working on it.
Have a nice christmas and a happy new year.
all the best
Marco
thanks for your answer.
I 'll keep working on it.
Have a nice christmas and a happy new year.
all the best
Marco
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