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self-assembly of polymers
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9 years 8 months ago #4008
by Mousumi
self-assembly of polymers was created by Mousumi
Hi,
Good evening.
I have a polymer with radius of gyration around 5 nm. I am trying to study the selfassemly of multiple chains of the same polymer using the Martini CG simulations. First a random configuration was created by inserting 35 polymers in a 40 nm box and then solvated with Martini W beads surrounding the molecules in at least 1 nm of thickness from the edge of a dodecahedron box. Naturally, to achieve this, it increased the box dimension to 53 nm. I was wondering whether I am doing it right!? After running until 70 ns I do not see any progress in the process of self-assembly though. I know I should run it for much longer time to get any result, however I would be grateful if you let me know if there is anything wrong in my steps.
As it is my first step into the CGing as well as self-assembling lack of experience in this field preventing me to be confident enough about my steps, especially with the box dimensions. Whatever previous research articles or Martini tutorial I read that indicates to me that the box volume should not be too big. The molecules are crowded inside the box without much spacing between them. Instead in my case the box is large and polymers are separated with enough space. So I was wondering what could be the optimum box dimension and how to achieve it? By trial and error? If anyone could give any expert insights regarding this I would be very grateful.
Thanks in advance.
Best regards,
Mousumi
Good evening.
I have a polymer with radius of gyration around 5 nm. I am trying to study the selfassemly of multiple chains of the same polymer using the Martini CG simulations. First a random configuration was created by inserting 35 polymers in a 40 nm box and then solvated with Martini W beads surrounding the molecules in at least 1 nm of thickness from the edge of a dodecahedron box. Naturally, to achieve this, it increased the box dimension to 53 nm. I was wondering whether I am doing it right!? After running until 70 ns I do not see any progress in the process of self-assembly though. I know I should run it for much longer time to get any result, however I would be grateful if you let me know if there is anything wrong in my steps.
As it is my first step into the CGing as well as self-assembling lack of experience in this field preventing me to be confident enough about my steps, especially with the box dimensions. Whatever previous research articles or Martini tutorial I read that indicates to me that the box volume should not be too big. The molecules are crowded inside the box without much spacing between them. Instead in my case the box is large and polymers are separated with enough space. So I was wondering what could be the optimum box dimension and how to achieve it? By trial and error? If anyone could give any expert insights regarding this I would be very grateful.
Thanks in advance.
Best regards,
Mousumi
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9 years 8 months ago #4009
by mnmelo
Replied by mnmelo on topic self-assembly of polymers
Hello,
It isn't entirely clear to me how you are adding the waters. If you are following the setup in the bilayer self-assembly tutorial , then there should be no volume change upon solvation, only upon running the system.
If instead you really are just adding an extra layer of water around a clump of polymer I'd say you're taking the wrong approach: the system will start off already phase-separated, likely in an unrealistic way, and might take a long time to equilibrate to where it should. Do as in the bilayer tutorial : decide on a box size; populate it with polymer; add water (you may need to restart using a larger box if you can't get all the waters you want to fit in).
As to whether the sizes are correct, it really depends on your system and what you want to study once it does self-assemble, but here are some notes:
- in your self-assembly simulation, the size of the box has to be large enough not to have molecules seeing themselves over the periodicity. Ideally, solvent molecules should also not interact with different images of the same molecule. These are the basic requirements but there are processes that might need larger systems (for instance, low-frequency modes of bilayer undulations).
- there is no upper bound on system size other than that dictated by your resources. Beware that the convergence of some events will also take longer the larger the system gets.
- self-assembly or aggregation events can depend on concentration. Therefore add water proportionally to the number of polymer chains (n waters per polymer) rather than "1 nm of thickness from the edge of a dodecahedron box". This way results should be comparable, concentration-wise, when run at different sizes.
It isn't entirely clear to me how you are adding the waters. If you are following the setup in the bilayer self-assembly tutorial , then there should be no volume change upon solvation, only upon running the system.
If instead you really are just adding an extra layer of water around a clump of polymer I'd say you're taking the wrong approach: the system will start off already phase-separated, likely in an unrealistic way, and might take a long time to equilibrate to where it should. Do as in the bilayer tutorial : decide on a box size; populate it with polymer; add water (you may need to restart using a larger box if you can't get all the waters you want to fit in).
As to whether the sizes are correct, it really depends on your system and what you want to study once it does self-assemble, but here are some notes:
- in your self-assembly simulation, the size of the box has to be large enough not to have molecules seeing themselves over the periodicity. Ideally, solvent molecules should also not interact with different images of the same molecule. These are the basic requirements but there are processes that might need larger systems (for instance, low-frequency modes of bilayer undulations).
- there is no upper bound on system size other than that dictated by your resources. Beware that the convergence of some events will also take longer the larger the system gets.
- self-assembly or aggregation events can depend on concentration. Therefore add water proportionally to the number of polymer chains (n waters per polymer) rather than "1 nm of thickness from the edge of a dodecahedron box". This way results should be comparable, concentration-wise, when run at different sizes.
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9 years 8 months ago #4010
by Mousumi
Replied by Mousumi on topic self-assembly of polymers
Thanks a lot for your expert suggestions. Now things are getting clear to me.
Best regards!
Best regards!
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