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specification of salt concentration
- liguo_UCAS
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1 year 8 months ago #9474
by liguo_UCAS
specification of salt concentration was created by liguo_UCAS
I have a question about the tutorial (Martini 3 Proteins - Part I: Basic and Martinize 2). I'm little confused about this discussion "Be careful in case you use strategies based on gmx genion. As each Martini water bead represents 4 water molecules, the concentration specified needs to be adapted to properly represent the target salt concentration".
I know that in Insane.py the salt concentration is determined by the relative number between water and salt ion, and every water bead replaced by salt ion bead represent 4 water molecules. But in genion -conc, the specified concentration is computed from the cell volume in the input tpr file which wouln't change when waters are replaced, So I don't know how should we adjust the specified concentration to properly represent the target salt concentration. Or do you mean that the specified concentration should be adapted to make sure the salt ion beads number computed from cell volume and adapted concentration in genion -conc could satisfy the target salt concentration determined by relative number between water and salt as in Insane.py?
I know that in Insane.py the salt concentration is determined by the relative number between water and salt ion, and every water bead replaced by salt ion bead represent 4 water molecules. But in genion -conc, the specified concentration is computed from the cell volume in the input tpr file which wouln't change when waters are replaced, So I don't know how should we adjust the specified concentration to properly represent the target salt concentration. Or do you mean that the specified concentration should be adapted to make sure the salt ion beads number computed from cell volume and adapted concentration in genion -conc could satisfy the target salt concentration determined by relative number between water and salt as in Insane.py?
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- riccardo
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1 year 8 months ago #9476
by riccardo
Replied by riccardo on topic specification of salt concentration
I think the latter option is what is meant ("the specified concentration should be adapted to make sure the salt ion beads number computed from cell volume and adapted concentration in genion -conc could satisfy the target salt concentration determined by relative number between water and salt as in Insane.py"). I think the recommended way to go about salt conc. is based on the relative number of water and ions.
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1 year 8 months ago #9477
by liguo_UCAS
Replied by liguo_UCAS on topic specification of salt concentration
Yes, I agree with you.
It seems like in most cases, researchers don't consider this concentration adaptation?
It seems like in most cases, researchers don't consider this concentration adaptation?
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1 year 8 months ago #9478
by riccardo
Replied by riccardo on topic specification of salt concentration
I am not sure about that / I do not have the data to say that. But I can tell you that using the relative number of molecules (rather than the box volume) is the way to compute the concentration that the Martini developers recommend.
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1 year 8 months ago #9479
by liguo_UCAS
Replied by liguo_UCAS on topic specification of salt concentration
Okay, I see. It helps a lot.
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