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Water per lipid
- shakira
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3 years 10 months ago #8563
by shakira
Water per lipid was created by shakira
Hi
I have seen in many coarse grain simulation of lipid membrane systems using MARTINI FF using 42 water lipid ratio. However in some works 120 water per lipid and even more are used. Increasing the water ratio will increase the computational cost. I guess the system becomes more realistic with increased water hydration. Other than this is there any other reason why people go for higher water hydration in their modeled bilayer system.
I have seen in many coarse grain simulation of lipid membrane systems using MARTINI FF using 42 water lipid ratio. However in some works 120 water per lipid and even more are used. Increasing the water ratio will increase the computational cost. I guess the system becomes more realistic with increased water hydration. Other than this is there any other reason why people go for higher water hydration in their modeled bilayer system.
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- vainikka
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3 years 10 months ago #8579
by vainikka
Replied by vainikka on topic Water per lipid
Hi,
I have quite limited experience working with Martini lipids, so take the answer with a grain of salt:
There indeed appears to be an abundance of water to lipid ratios reported in the literature.
Is there a reason you would not want your system to be fully hydrated? I know some studies have used lower hydration levels to study permeation properties, and others have studied how the hydration levels affect the melting temperature of the bilayer.
If you don't have any special requirements for the hydration level, just use insane.py to create your system - that should make sure you end up with a reasonable setup.
I have quite limited experience working with Martini lipids, so take the answer with a grain of salt:
There indeed appears to be an abundance of water to lipid ratios reported in the literature.
Is there a reason you would not want your system to be fully hydrated? I know some studies have used lower hydration levels to study permeation properties, and others have studied how the hydration levels affect the melting temperature of the bilayer.
If you don't have any special requirements for the hydration level, just use insane.py to create your system - that should make sure you end up with a reasonable setup.
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- riccardo
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3 years 10 months ago #8580
by riccardo
Replied by riccardo on topic Water per lipid
Also not really a lipid expert here. I second the suggestion about insane.
For curiosity, I checked a few papers and I see that, e.g., in the Martini plasma membrane paper ( pubs.acs.org/doi/abs/10.1021/ja507832e ) a ratio >= 15 CG water beads per lipid (corresponding to >= 60 water molecules) is used and deemed as "ample water".
I suppose also that since there's no real "rule" on this, people may just have more water because computational resources are getting more abundant (and simply end up caring less about some more water in the system..).
For curiosity, I checked a few papers and I see that, e.g., in the Martini plasma membrane paper ( pubs.acs.org/doi/abs/10.1021/ja507832e ) a ratio >= 15 CG water beads per lipid (corresponding to >= 60 water molecules) is used and deemed as "ample water".
I suppose also that since there's no real "rule" on this, people may just have more water because computational resources are getting more abundant (and simply end up caring less about some more water in the system..).
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