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Modeling polypropylene (PP) sheet
- Junb
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2 years 5 months ago #9225
by Junb
Modeling polypropylene (PP) sheet was created by Junb
Dear,
I would really appreciate if someone can help with my issue below,
I am trying to build a PP sheet in its crystalline structure using MARTINI model with the PP forcefield, and model it with protein solution system.
However, I first modelled the PP sheet in vacuum condition or even solvent condition, the sheet just shrunk and lost its crystalline structure. I used periodic-molecules for this system, but it sill does not work (shrunk to a cluster).
I wonder how I can model PP sheet maintaining its crystalline structure. Thank you very much in advance.
I would really appreciate if someone can help with my issue below,
I am trying to build a PP sheet in its crystalline structure using MARTINI model with the PP forcefield, and model it with protein solution system.
However, I first modelled the PP sheet in vacuum condition or even solvent condition, the sheet just shrunk and lost its crystalline structure. I used periodic-molecules for this system, but it sill does not work (shrunk to a cluster).
I wonder how I can model PP sheet maintaining its crystalline structure. Thank you very much in advance.
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- riccardo
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2 years 4 months ago #9250
by riccardo
Replied by riccardo on topic Modeling polypropylene (PP) sheet
I have never tried to build such a system so my specific knowledge may be limited but let me throw some thoughts.
I'm not that surprised that in vacuum the system will tend to shrink. Are you doing an NVT simulation when in vacuum, by the way?
Does a similar system work at atomistic resolution? If so, did you try to forward-map that starting configuration to Martini?
If you just want the sheet of PP to stay in place, you can always think of using position restraints.
I'm not that surprised that in vacuum the system will tend to shrink. Are you doing an NVT simulation when in vacuum, by the way?
Does a similar system work at atomistic resolution? If so, did you try to forward-map that starting configuration to Martini?
If you just want the sheet of PP to stay in place, you can always think of using position restraints.
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- Junb
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2 years 4 months ago #9255
by Junb
Replied by Junb on topic Modeling polypropylene (PP) sheet
Hi Riccardo,
Thank you so much for your kind reply!
I did this vacuum system using NPT simulation. This is trying to mimic what people did in all-atom system, where they first simulated PP with several layers in vacuum condition, then interact with protein.
Yes, it worked for the all-atom system (title: Lysozyme Adsorption on Polyethylene Surfaces: Why Are Long Simulations Needed?). However, the area of this system is small, the protein I want to model is much larger than the protein used in this previous all-atom simulation.
Yes, you are correct! I used position restraint and it works for single-layer small PP surface, but not for multi-layers with larger area which is I really want to do.
Thank you so much for your kind reply!
I did this vacuum system using NPT simulation. This is trying to mimic what people did in all-atom system, where they first simulated PP with several layers in vacuum condition, then interact with protein.
Yes, it worked for the all-atom system (title: Lysozyme Adsorption on Polyethylene Surfaces: Why Are Long Simulations Needed?). However, the area of this system is small, the protein I want to model is much larger than the protein used in this previous all-atom simulation.
Yes, you are correct! I used position restraint and it works for single-layer small PP surface, but not for multi-layers with larger area which is I really want to do.
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- riccardo
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2 years 4 months ago #9257
by riccardo
Replied by riccardo on topic Modeling polypropylene (PP) sheet
I think if there's vacuum in the system it would be more appropriate to run in NVT conditions.
Why would the single-layer work and the multi-layer wouldn't? Aren't you applying position restraints to *all the PP particles* in both the single-layer case and multi-layer case?
Why would the single-layer work and the multi-layer wouldn't? Aren't you applying position restraints to *all the PP particles* in both the single-layer case and multi-layer case?
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- Junb
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2 years 4 months ago #9258
by Junb
Replied by Junb on topic Modeling polypropylene (PP) sheet
Thanks again Riccardo for your kind reply.
Yes, I applied restraints to all of them. I think the issue is I am not clear about the distance between the layers. I did test different distances between layers, such as 0.3, 0.5, 0.7 nm, and I think if the distance larger than 1 nm? some water will flow into the space between those layers.
Yes, I applied restraints to all of them. I think the issue is I am not clear about the distance between the layers. I did test different distances between layers, such as 0.3, 0.5, 0.7 nm, and I think if the distance larger than 1 nm? some water will flow into the space between those layers.
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2 years 2 months ago #9304
by riccardo
Replied by riccardo on topic Modeling polypropylene (PP) sheet
Not sure if this is still relevant, sorry for the delay but I missed this.
Right, so if the problem is finding the optimal distance between the sheets, you could either try many different setups or - probably better - equilibrate a bulk multi-layered system (without vacuum, in NPT conditions) to figure out what's the equilibrium distance between the sheets.
Right, so if the problem is finding the optimal distance between the sheets, you could either try many different setups or - probably better - equilibrate a bulk multi-layered system (without vacuum, in NPT conditions) to figure out what's the equilibrium distance between the sheets.
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2 years 2 months ago #9305
by Junb
Replied by Junb on topic Modeling polypropylene (PP) sheet
No worries. I have already appreciated your time and kind reply to help with question. Yes, I will try as you suggested then to see if that can help. Thanks a lot.
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