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Self-Assembly: different pressure control
- mferraro
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10 years 7 months ago #1943
by mferraro
Self-Assembly: different pressure control was created by mferraro
Hi everybody,
I 'd like to ask you something about the choice of pressure control when running self-assembly.
Having a look at standard mdp files for the raft (raft.mdp) and tutorial on self-assembly, I saw differences in the pressure control chosen for these two system.
DSPC bilayer has been assembled in ISOTROPIC conditions, whereas the raft has been simulated in SEMI-ISOTROPIC ones.
Clearly, I realize that initial configurations for the two systems are different too; in fact for DSPC bilayer you suggest a cubic box with randomly placed lipids, while for the raft a pre-equilibrated patch has been used whose lipid types has been changed to generate raft-like mixture.
In my case I assembled both a system containing only lipids and another one containing also a protein and I'm wondering if pressure control in these two models have to be different due to the presence of the peptide. My starting box has the same magnitude in x-y dimensions but a different one in Z-dimension. In the system containing protein I think that the semi-isotropic control should be used (shouldn't be?), but without protein I don't know what it's better to do. The major doubt comes from the fact that I start from a random configuration of lipids and water that are free to evolve in a bilayer (so probably I do not have to impose a direction coupling x-y axes, because it should find it by itself). On the other side, I actually drive the process choosing a rectangular box (avoiding the formation of multiple bilayers spaced by slabs of water), so probably semi-isotropic control could be good as well.
Could you kindly make this aspect clearer?
Thanks very much in advance for your precious suggestions!
Maria.
I 'd like to ask you something about the choice of pressure control when running self-assembly.
Having a look at standard mdp files for the raft (raft.mdp) and tutorial on self-assembly, I saw differences in the pressure control chosen for these two system.
DSPC bilayer has been assembled in ISOTROPIC conditions, whereas the raft has been simulated in SEMI-ISOTROPIC ones.
Clearly, I realize that initial configurations for the two systems are different too; in fact for DSPC bilayer you suggest a cubic box with randomly placed lipids, while for the raft a pre-equilibrated patch has been used whose lipid types has been changed to generate raft-like mixture.
In my case I assembled both a system containing only lipids and another one containing also a protein and I'm wondering if pressure control in these two models have to be different due to the presence of the peptide. My starting box has the same magnitude in x-y dimensions but a different one in Z-dimension. In the system containing protein I think that the semi-isotropic control should be used (shouldn't be?), but without protein I don't know what it's better to do. The major doubt comes from the fact that I start from a random configuration of lipids and water that are free to evolve in a bilayer (so probably I do not have to impose a direction coupling x-y axes, because it should find it by itself). On the other side, I actually drive the process choosing a rectangular box (avoiding the formation of multiple bilayers spaced by slabs of water), so probably semi-isotropic control could be good as well.
Could you kindly make this aspect clearer?
Thanks very much in advance for your precious suggestions!
Maria.
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- djurre
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10 years 7 months ago #1950
by djurre
Replied by djurre on topic Self-Assembly: different pressure control
In general, you need semi-isotropic if you have an elastic object (like a bilayer) spanning the box in the x and/or y direction. So, if you have bilayer: you need semi-isotropic coupling. If the bilayer is still forming, you want isotropoic coupling. At some point you need to stop the simulation, change pressure couplilng and restart. If you only have a (soluble) protein, you want to use isotropic coupling. If you have a membrane protein, you use semi-isotropic coupling.
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- mferraro
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10 years 7 months ago #1952
by mferraro
Replied by mferraro on topic Self-Assembly: different pressure control
Thank you so much Djurre!!!
Maria.
Maria.
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