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Water layer in membrane proteines system
- Robin
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7 years 9 months ago #5708
by Robin
Water layer in membrane proteines system was created by Robin
Hello,
I used the program insane.py in order to insert 2 proteins in a POPC/CHOL 10:1 membrane and to solvate my system. Since I didn't want to have too much waters in my system (for calculation time purpose), I solvated my system with the following squared box: x=20, y=20, Z=10nm (with water layers about 2nm each).
Looking at most membrane systems in tutorial and in these forums, I only found cubic systems with Z box length matching the X and Y axis. Could you please answer the following questions?
- Can a squared box with periodicity xyz give trouble for long simulation?
- Is a 2nm water layer enough to represent the water surrounding the membrane?
- Finally, I found that insane.py didn't put an equal quantity of water molecule for upper and lower water layer (4 sheet of water top, 5 bot). Can it become a problem later in simulation?
I hope someone will enlighten me :).
Robin
I used the program insane.py in order to insert 2 proteins in a POPC/CHOL 10:1 membrane and to solvate my system. Since I didn't want to have too much waters in my system (for calculation time purpose), I solvated my system with the following squared box: x=20, y=20, Z=10nm (with water layers about 2nm each).
Looking at most membrane systems in tutorial and in these forums, I only found cubic systems with Z box length matching the X and Y axis. Could you please answer the following questions?
- Can a squared box with periodicity xyz give trouble for long simulation?
- Is a 2nm water layer enough to represent the water surrounding the membrane?
- Finally, I found that insane.py didn't put an equal quantity of water molecule for upper and lower water layer (4 sheet of water top, 5 bot). Can it become a problem later in simulation?
I hope someone will enlighten me :).
Robin
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- peterkroon
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7 years 9 months ago #5710
by peterkroon
Replied by peterkroon on topic Water layer in membrane proteines system
Hi,
Note: I don't work with membranes
A rectangular (or is it triclinic?) (rather than cubic) box should not be a problem, but you may run in to troubles if your membrane undulates too much and starts to interact with it's periodic image - you'll end up with pretty hexagonal images if this happens. You can try to impose a flatbottomed potential across the Z axis to prevent this, but consult an expert.
As for the last question: your box is periodic in Z, so you can't distinguish the upper from the lower water layer.
Peter
Note: I don't work with membranes
A rectangular (or is it triclinic?) (rather than cubic) box should not be a problem, but you may run in to troubles if your membrane undulates too much and starts to interact with it's periodic image - you'll end up with pretty hexagonal images if this happens. You can try to impose a flatbottomed potential across the Z axis to prevent this, but consult an expert.
As for the last question: your box is periodic in Z, so you can't distinguish the upper from the lower water layer.
Peter
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- Robin
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7 years 9 months ago #5711
by Robin
Replied by Robin on topic Water layer in membrane proteines system
Hi Peter,
Thank you very much for your quick reply.
Yes, my system is rectangular. From a colleague working on lipids, I heard that I shouldn't see too much ondulation. At 1 microsecond simulation, I can't see any interaction between the Z axis periodic images.
Yes, as you said, it's in fact logical that I can't distinguish upper from lower water layer (thank you for pointing that out).
Have a good day, mine is already better thanks to you :).
Robin
Thank you very much for your quick reply.
Yes, my system is rectangular. From a colleague working on lipids, I heard that I shouldn't see too much ondulation. At 1 microsecond simulation, I can't see any interaction between the Z axis periodic images.
Yes, as you said, it's in fact logical that I can't distinguish upper from lower water layer (thank you for pointing that out).
Have a good day, mine is already better thanks to you :).
Robin
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