normal Naproxen parameters

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1 month 4 days ago - 1 month 4 days ago #7518 by riccardo
riccardo replied the topic: Naproxen parameters
Pim's right (thanks for noticing!).

Here is how I would map it:

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The wavy line is a bond (k=1250 would be good), the other constraints. You'll then need one improper dihedral SC5-SC5-SN0-SC5 to keep the naphthalene-like moiety flat, plus a couple of angles for the Qd bead (2x Qd-SC5-SC5 -- I guess you can re-use some of the ones you defined). I would also exclude nonbonded interactions between the top-left SC5 and bottom-right SC5 beads. So 1 bond, 5 constraints, 1 improper dihedral and 2 angles should be enough.

Let me know if something is not clear.
Last Edit: 1 month 4 days ago by riccardo.

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1 month 4 days ago #7521 by ric.concu
ric.concu replied the topic: Naproxen parameters
Dear Riccardo,
thank you so much for your kind help. Yes, everything it is quite clear, I will take your advices while mapping the Naproxen. I have only one doubt, why do you map the bottom left bead as SN0 and not, for example SC4 or SC3? Do you think that the -OCH3 terminal is so relevant against the SC of the naftalen moiety?

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1 month 4 days ago #7522 by bart
bart replied the topic: Naproxen parameters
Why not Nad for the bottom left? Couldn't it be donor and acceptor? Maybe I am missing something obvious here, but I am curious what that is.

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1 month 3 days ago - 1 month 3 days ago #7526 by riccardo
riccardo replied the topic: Naproxen parameters
Sorry, my drawing was wrong (may have misled Bart). The bottom-left substituent on the naphthalene is a -OCH3 group, not a -OH.

Methoxy/ether groups are usually mapped with N0 beads. At most the -OCH3 group could be a h-bond acceptor (Na) I would say. I considered the bead I placed to be 1/2 benzene-like and 1/2 methoxy like. Benzene is SC5, methoxy is N0 (at least), so I don't see why one would opt for a more hydrophobic SC4/3 bead.

In any case, of course the best would be to validate the bead choices against free energy of transfer data (if any are available).
Last Edit: 1 month 3 days ago by riccardo.

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1 month 3 days ago - 1 month 3 days ago #7527 by ric.concu
ric.concu replied the topic: Naproxen parameters
Yes, after reviewing the tables I think you are right and I would think that the -OCH3 would be better represented by a N0 bead instead of a Na.
Last Edit: 1 month 3 days ago by ric.concu.

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1 month 3 days ago #7528 by ric.concu
ric.concu replied the topic: Naproxen parameters
Dear Riccardo, now it seems working fine; however, it's not really clear for me how you choose to define only one bond and the others as contraints. Thanl you so much one more time for your kind help.

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1 month 2 days ago #7529 by riccardo
riccardo replied the topic: Naproxen parameters
I proposed to define those as constraints because usually the distributions of bonds between "aromatic" beads (i.e., beads representing group of atoms which are part of aromatic rings) are rather narrow (i.e., highly localized). Thus, they'd require a very stiff potential (i.e., very stiff bonds with k ~ 1000000), which in turn would require short time steps to sample their oscillations appropriately. But at the Martini scale these oscillations are actually unimportant and therefore we replace the (stiff) bonds with constraints. Have a look, for example, at the benzene model (3 x SC5 beads with 3 constraints).

You could have a look yourself. Take the atomistic model of naproxen, plot the distribution for the distance between the centers of mass of the two top moieties (the two top SC5 beads), and compare it to the distributions for two versions of your CG model: one with constraints, one with (stiff) bonds.

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1 month 2 days ago #7530 by bart
bart replied the topic: Naproxen parameters
Jup that was it, thanks :)

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1 month 2 days ago #7531 by ric.concu
ric.concu replied the topic: Naproxen parameters
Dear,
one more time thank you for your advice, now everyting is clearer.
I previously mapped the napthalen moiety using a 5 beads mapping considering for instance the benzene model.
I will prepare a short run to compare the two models.

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