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Modeling Polymers - AA Models for Bonded Parametrization
- TravisM
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4 years 2 months ago #8415
by TravisM
Modeling Polymers - AA Models for Bonded Parametrization was created by TravisM
Hello all,
I am working to build some CG Martini Models of polymers. I am currently working on trying to get an AA simulation from which I can parameterize the bonded interactions. I am curious if anyone has any recommendations for the process for creating these AA models. Based on literature/internet searches, the basic pipeline I've gathered so far is:
1. Create pdb files of monomer subunits using Avogadro
2. Use Assemble! to create polymer architecture from monomer pdb files.
3. Use ATB to generate topology files from polymer structure files from Assemble!
I am looking to get feedback from others who have done similar things to see if this is an appropriate workflow, or if there are better/more efficient means of generating the topology and structure files for the AA simulation. I am brand new to MD simulations, so any help/advice would be greatly appreciated.
Thanks!
Travis
I am working to build some CG Martini Models of polymers. I am currently working on trying to get an AA simulation from which I can parameterize the bonded interactions. I am curious if anyone has any recommendations for the process for creating these AA models. Based on literature/internet searches, the basic pipeline I've gathered so far is:
1. Create pdb files of monomer subunits using Avogadro
2. Use Assemble! to create polymer architecture from monomer pdb files.
3. Use ATB to generate topology files from polymer structure files from Assemble!
I am looking to get feedback from others who have done similar things to see if this is an appropriate workflow, or if there are better/more efficient means of generating the topology and structure files for the AA simulation. I am brand new to MD simulations, so any help/advice would be greatly appreciated.
Thanks!
Travis
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- riccardo
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4 years 2 months ago #8416
by riccardo
Replied by riccardo on topic Modeling Polymers - AA Models for Bonded Parametrization
Hi Travis,
I'm not familiar with "Assemble!" so can't tell you much about that.
In general, developing an atomistic model for a polymer can be quite some work. But, of course, it always depends on how accurate you want it to be and on what you want to do with it.
I would also say that there's no single clear-cut protocol to do that, as far as I know.
For now, I would recommend to have a look at the Martini polymer models available here: cgmartini.nl/index.php/force-field-parameters/polymers (e.g., pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b04760 , pubs.rsc.org/en/content/articlehtml/2011/sm/c0sm00481b , pubs.acs.org/doi/abs/10.1021/jacs.6b11717 , etc.) and dig into the papers to see how the different authors dealt with getting the bonded parameters from an atomistic reference model. I would already highlight that, for validating the eventual Martini polymer model, some experimental data to use as reference would be very beneficial (e.g., radius of gyration in (different) solvent(s), etc.).
I'm not familiar with "Assemble!" so can't tell you much about that.
In general, developing an atomistic model for a polymer can be quite some work. But, of course, it always depends on how accurate you want it to be and on what you want to do with it.
I would also say that there's no single clear-cut protocol to do that, as far as I know.
For now, I would recommend to have a look at the Martini polymer models available here: cgmartini.nl/index.php/force-field-parameters/polymers (e.g., pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b04760 , pubs.rsc.org/en/content/articlehtml/2011/sm/c0sm00481b , pubs.acs.org/doi/abs/10.1021/jacs.6b11717 , etc.) and dig into the papers to see how the different authors dealt with getting the bonded parameters from an atomistic reference model. I would already highlight that, for validating the eventual Martini polymer model, some experimental data to use as reference would be very beneficial (e.g., radius of gyration in (different) solvent(s), etc.).
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