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matinimize a Polysalfone chain
- diaobk
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8 years 4 months ago #5327
by diaobk
matinimize a Polysalfone chain was created by diaobk
Dear all
I am trying to matinimize a Polysalfone chain.
The structure:
-[O-C6H4-C(CH3)2-C6H4-O-C6H4-SO2-C6H4]-
1.
How should I define the SO2 group? It's a proton acceptor, but seems more polar than nomal Na partical(C=O,etc)
2.
The BENZENE ring is described by 3 beads in martini model，but I want to add different side chains on the benzene, with a triangle structure, the links between benzenes and side chains will be very complex.
I use only one bead now to represent a benzene and half the O nearby. Was this reasonable?
Should I increase the benzene to a BC5 type just like the BP4 water?
Or another map strategy：
c (c-c) (c-c) o
(c-c-c) (c-o-c) (c-s-c)
c (c-c) (c-c) o
use two beads in parallel, give the remained C to link atoms?
I am trying to matinimize a Polysalfone chain.
The structure:
-[O-C6H4-C(CH3)2-C6H4-O-C6H4-SO2-C6H4]-
1.
How should I define the SO2 group? It's a proton acceptor, but seems more polar than nomal Na partical(C=O,etc)
2.
The BENZENE ring is described by 3 beads in martini model，but I want to add different side chains on the benzene, with a triangle structure, the links between benzenes and side chains will be very complex.
I use only one bead now to represent a benzene and half the O nearby. Was this reasonable?
Should I increase the benzene to a BC5 type just like the BP4 water?
Or another map strategy：
c (c-c) (c-c) o
(c-c-c) (c-o-c) (c-s-c)
c (c-c) (c-c) o
use two beads in parallel, give the remained C to link atoms?
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- siewert
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8 years 4 months ago #5329
by siewert
Replied by siewert on topic matinimize a Polysalfone chain
Hi,
for the SO2, you can use a more polar particle type (like P1) if you think it is more polar
(ideally, you have partitioning data to support your claim).
for the mapping, I would group the C(CH3)2 and SO2 into a single, normal sized bead, and do the same for the C-O-C unit (where the C's are from the adjacent benzene groups). This leaves you with 5 C atoms left on each benzene unit, and those can be mapped to two SC5 particles. Together with the C-O-C bead you keep the triangular nature of the benzene groups this way.
Good luck!
Siewert-Jan
for the SO2, you can use a more polar particle type (like P1) if you think it is more polar
(ideally, you have partitioning data to support your claim).
for the mapping, I would group the C(CH3)2 and SO2 into a single, normal sized bead, and do the same for the C-O-C unit (where the C's are from the adjacent benzene groups). This leaves you with 5 C atoms left on each benzene unit, and those can be mapped to two SC5 particles. Together with the C-O-C bead you keep the triangular nature of the benzene groups this way.
Good luck!
Siewert-Jan
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- Pim
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8 years 4 months ago #5330
by Pim
Replied by Pim on topic matinimize a Polysalfone chain
I'd agree, it makes it especially nice if you would then like to add substituents to your benzene rings, it would keep symmetry that way. If the substituents are small, you could choose other particle types for the ring beads: for example SP1 for an -OH group like in the amino acid tyrosine. If the substituents have >3 heavy atoms, you'll have to start adding beads, but I'd avoid that if you can.
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- diaobk
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8 years 4 months ago #5335
by diaobk
Replied by diaobk on topic matinimize a Polysalfone chain
Where should I put the two SC5 particles?
I learned that "benzene is one of those special cases where the positions of the beads are not directly based on the centers of mass"
With C(CH3)2 and SO2 on the other side, a square is formed actually. More angles and dihedrals will appear.
And unfortunately, I have quite long side chains in my system.
Our interest focus on a larger distance scale. I want to get a cg structure as simple as possible without much lose of information.
Can atoms be used duplicately in mapping cg centers?
To get cg centers along the chain, I used twice the C in benzene connected to C(CH3)2 or SO2.
This image is hidden for guests.
This could be explained in another map:
O-C6-C(C2)-C6-O-C6-SO2==>COC -C4- C-C(C2)-C C4 C-O-C C4 C-SO2-C
While the remaining C4 in benzene is so close, COC group could be neglected.
(Maybe I should add it back if this map sounds reasonable.)
I learned that "benzene is one of those special cases where the positions of the beads are not directly based on the centers of mass"
With C(CH3)2 and SO2 on the other side, a square is formed actually. More angles and dihedrals will appear.
And unfortunately, I have quite long side chains in my system.
Our interest focus on a larger distance scale. I want to get a cg structure as simple as possible without much lose of information.
Can atoms be used duplicately in mapping cg centers?
To get cg centers along the chain, I used twice the C in benzene connected to C(CH3)2 or SO2.
This image is hidden for guests.
Please log in or register to see it.
This could be explained in another map:
O-C6-C(C2)-C6-O-C6-SO2==>COC -C4- C-C(C2)-C C4 C-O-C C4 C-SO2-C
While the remaining C4 in benzene is so close, COC group could be neglected.
(Maybe I should add it back if this map sounds reasonable.)
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- Pim
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8 years 4 months ago - 8 years 4 months ago #5336
by Pim
Replied by Pim on topic matinimize a Polysalfone chain
I suppose the stacking of the aromatic rings is going to be important also on the large scale, so I'd recommend using to S-type particles for the C4 group in your mapping, COC -2*SC- C-C(C2)-C 2*SC C-O-C 2*SC-SO2-C. It is not a problem to use atoms multiple times to assign bead positions as long as you avoid overmapping.
Indeed this will give you squares in your bonded parameters and to keep the planarity that's a bit trickier. If you don't want angle / dihedral constraints you will have to constrain opposite corners of the square with a bond. In any case, you're going to need a high lincs-order. Nonetheless it seems like the most realistic mapping for your polymer. Perhaps, if the above isn't working for you, you can think about virtual sites as in, for example, cholesterol.
Indeed this will give you squares in your bonded parameters and to keep the planarity that's a bit trickier. If you don't want angle / dihedral constraints you will have to constrain opposite corners of the square with a bond. In any case, you're going to need a high lincs-order. Nonetheless it seems like the most realistic mapping for your polymer. Perhaps, if the above isn't working for you, you can think about virtual sites as in, for example, cholesterol.
Last edit: 8 years 4 months ago by Pim.
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