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Applying an electric field on lipids
- Sithara Perera
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6 years 5 months ago #7429
by Sithara Perera
Applying an electric field on lipids was created by Sithara Perera
I'm doing molecular dynamic simulations of protein interaction with lipid bi layers using CGmartini force fields under an electric field.
But when I apply the electric field and simulated for 50 ns under -0.7mV/nm, the bi layer moves in the electric field and then eventually reaches the bottom of simulation box. So it is not possible to see the protein interaction with the bi layer. I tried applying position restrains on z axis, but then the box dimensions started to change
The bi layer a 512DPPC bi layer.
What can I do to fix this??
But when I apply the electric field and simulated for 50 ns under -0.7mV/nm, the bi layer moves in the electric field and then eventually reaches the bottom of simulation box. So it is not possible to see the protein interaction with the bi layer. I tried applying position restrains on z axis, but then the box dimensions started to change
The bi layer a 512DPPC bi layer.
What can I do to fix this??
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- bart
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6 years 5 months ago #7433
by bart
Replied by bart on topic Applying an electric field on lipids
Hello,
I think you are on the right path. Be aware that you use semiisotropic coupling and I would advice on using a flat bottomed potential for restricting the bilayer movement in z. The fact that your box starts to change is not very surprising, for your bilayer's charged particles start to interact with the electric field. This might very well have an effect on the lateral pressure (as an effect APL increases as well under NPT conditions).
Cheers and if you still have problems please let me know,
Bart
I think you are on the right path. Be aware that you use semiisotropic coupling and I would advice on using a flat bottomed potential for restricting the bilayer movement in z. The fact that your box starts to change is not very surprising, for your bilayer's charged particles start to interact with the electric field. This might very well have an effect on the lateral pressure (as an effect APL increases as well under NPT conditions).
Cheers and if you still have problems please let me know,
Bart
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- peterkroon
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6 years 5 months ago #7434
by peterkroon
Replied by peterkroon on topic Applying an electric field on lipids
First off, your box doesn't have a bottom, since it's periodic (so I'm not sure there's a problem)
You can try a more aggresive COM motion removal, or post this to the Gromacs userlist.
You can try a more aggresive COM motion removal, or post this to the Gromacs userlist.
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