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How to characterize block copolymer (PEG polymer with branches)?
- ps2pspgood
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2 years 2 months ago #9297
by ps2pspgood
How to characterize block copolymer (PEG polymer with branches)? was created by ps2pspgood
Hi,
I am new to the CG model simulation. I was using all atom MD simulation with Desmond. I would like to study the process of endosome escape, but all atom simulation is too slow.
My model basically containing 2 part. The first one is the endosome lipid bilayer (I obtained from this reference: A molecular view on the escape of lipoplexed DNA from the endosome). The second part is my polymers. One is Polyethyleneimine and the other one is PEG block copolymer (It is shown in the following figure).
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I would like to know how to parametrize it and generate topology file that can be used in martini force field.
Could you give me some guides and hints on how to walk through the process including choosing suitable beads and parameters?
Thank you very much for your great help.
I am new to the CG model simulation. I was using all atom MD simulation with Desmond. I would like to study the process of endosome escape, but all atom simulation is too slow.
My model basically containing 2 part. The first one is the endosome lipid bilayer (I obtained from this reference: A molecular view on the escape of lipoplexed DNA from the endosome). The second part is my polymers. One is Polyethyleneimine and the other one is PEG block copolymer (It is shown in the following figure).
This image is hidden for guests.
Please log in or register to see it.
I would like to know how to parametrize it and generate topology file that can be used in martini force field.
Could you give me some guides and hints on how to walk through the process including choosing suitable beads and parameters?
Thank you very much for your great help.
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- fgrunewald
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2 years 2 months ago #9298
by fgrunewald
Replied by fgrunewald on topic How to characterize block copolymer (PEG polymer with branches)?
Hi,
That's an interesting problem. Luckily for you we have several bits and pieces already done. I would recommend you approach your project in Martini2 for which a good PEG model has already been parametrized ( pubs.acs.org/doi/10.1021/acs.jpcb.8b04760 ). There exists also several versions of Polyethyleneimine in Martini2, but you have to look in the literature for it. Once you have these components you just have to derive parameters for the branch attached to the PEG chain. For that you can follow the steps in this tutorial ( cgmartini.nl/index.php/tutorials-general...orials-polymers-gmx5 ).
To generate the topologies with branching you can use the polyply tool ( github.com/marrink-lab/polyply_1.0 ) that has been developed exactly for this purpose. Tutorials for polyply are available on the GitHub website. However, if you need more assistance you can also take your question to the polyply discussions board ( github.com/marrink-lab/polyply_1.0/discussions ).
Good Luck!
That's an interesting problem. Luckily for you we have several bits and pieces already done. I would recommend you approach your project in Martini2 for which a good PEG model has already been parametrized ( pubs.acs.org/doi/10.1021/acs.jpcb.8b04760 ). There exists also several versions of Polyethyleneimine in Martini2, but you have to look in the literature for it. Once you have these components you just have to derive parameters for the branch attached to the PEG chain. For that you can follow the steps in this tutorial ( cgmartini.nl/index.php/tutorials-general...orials-polymers-gmx5 ).
To generate the topologies with branching you can use the polyply tool ( github.com/marrink-lab/polyply_1.0 ) that has been developed exactly for this purpose. Tutorials for polyply are available on the GitHub website. However, if you need more assistance you can also take your question to the polyply discussions board ( github.com/marrink-lab/polyply_1.0/discussions ).
Good Luck!
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- ps2pspgood
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2 years 2 months ago - 2 years 2 months ago #9301
by ps2pspgood
Replied by ps2pspgood on topic How to characterize block copolymer (PEG polymer with branches)?
Thank you very much for your great support.
I will try to construct the model based on your suggestion.
So will you suggest to use Matini2 over the newer version 3?
Also I found that we have martini2.2P and martini2.3P. What is the difference.
I look into the tutorial that you posted.
I thought my workflow will be: (could you give advice for me?)
(1) Get the parameter of PEG from the paper. (How to incorporate into martini input parameter?)
(2) Parameterization of side chains. (I understand the main principle of fitting the CG model to the atomistic trajectory. How to get the beads parameterization for side chains?) First, define the scheme of beads. Run the atomistic MD simulation. In this step, do I need to use the whole PEGGly molecules? What kind of system do I need to set up? Then, fit the results like the method in the tutorial. Additionally, I found there is a table for suggesting the selection of beads. Is there any predefined beads for molecules? Can I just choose the beads without reparametrizing?
(3) Construction of endosome lipid CG model. I will take the constructed model from paper. However, could you suggest a tutorial for constructing of lipid bilayer tutorial from the beginning?
(4) Run CG simulation for PEG and lipid to obtain a stable conformation.
(5) Construct the simulation system box. Could you suggest tutorial on this also? I use Gromacs before to set up a simple MD simulation in a water box. How do I place lipid and PEG polymer into a box filled with water?
(6) Run equilibrium and MD production with Gromacs
(7) Analyze the trajectory.
I am very new to this field and try to learn this on my own.
Sorry for many questions.
Thank you again for the help!
I will try to construct the model based on your suggestion.
So will you suggest to use Matini2 over the newer version 3?
Also I found that we have martini2.2P and martini2.3P. What is the difference.
I look into the tutorial that you posted.
I thought my workflow will be: (could you give advice for me?)
(1) Get the parameter of PEG from the paper. (How to incorporate into martini input parameter?)
(2) Parameterization of side chains. (I understand the main principle of fitting the CG model to the atomistic trajectory. How to get the beads parameterization for side chains?) First, define the scheme of beads. Run the atomistic MD simulation. In this step, do I need to use the whole PEGGly molecules? What kind of system do I need to set up? Then, fit the results like the method in the tutorial. Additionally, I found there is a table for suggesting the selection of beads. Is there any predefined beads for molecules? Can I just choose the beads without reparametrizing?
(3) Construction of endosome lipid CG model. I will take the constructed model from paper. However, could you suggest a tutorial for constructing of lipid bilayer tutorial from the beginning?
(4) Run CG simulation for PEG and lipid to obtain a stable conformation.
(5) Construct the simulation system box. Could you suggest tutorial on this also? I use Gromacs before to set up a simple MD simulation in a water box. How do I place lipid and PEG polymer into a box filled with water?
(6) Run equilibrium and MD production with Gromacs
(7) Analyze the trajectory.
I am very new to this field and try to learn this on my own.
Sorry for many questions.
Thank you again for the help!
Last edit: 2 years 2 months ago by ps2pspgood. Reason: make the question more specific.
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