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Martini simulation of a bilayer with a wall
- LJefferys
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8 years 1 day ago #5533
by LJefferys
Martini simulation of a bilayer with a wall was created by LJefferys
Hi,
I was wondering if anyone has run simulations of a lipid bilayer using Martini with one or two walls? I am trying to set up such a simulation, but every attempt at equilibrating the system with a wall leads to the system blowing up. I cannot find any example parameters that anyone has used for a wall in Martini to use as a starting point for this...any help would be really appreciated!
Best wishes,
Lizzie
I was wondering if anyone has run simulations of a lipid bilayer using Martini with one or two walls? I am trying to set up such a simulation, but every attempt at equilibrating the system with a wall leads to the system blowing up. I cannot find any example parameters that anyone has used for a wall in Martini to use as a starting point for this...any help would be really appreciated!
Best wishes,
Lizzie
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- mnmelo
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7 years 11 months ago #5539
by mnmelo
Replied by mnmelo on topic Martini simulation of a bilayer with a wall
Hi Lizzie,
Using the typical GROMACS walls can indeed be tricky and artifact-prone. We've had success recently using the new flat-bottomed potentials in GROMACS 5.1. These are much easier to employ. If you're trying to make walls above and below the membrane all you need to do is to create a reference structure where all molecules that the potential affects are placed at the z of the bilayer center.
Give it a try and let us know if you need more help.
Cheers,
Manel
Using the typical GROMACS walls can indeed be tricky and artifact-prone. We've had success recently using the new flat-bottomed potentials in GROMACS 5.1. These are much easier to employ. If you're trying to make walls above and below the membrane all you need to do is to create a reference structure where all molecules that the potential affects are placed at the z of the bilayer center.
Give it a try and let us know if you need more help.
Cheers,
Manel
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- LJefferys
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7 years 11 months ago #5559
by LJefferys
Replied by LJefferys on topic Martini simulation of a bilayer with a wall
Hi,
Thanks! I will try that - I have not used Gromacs 5.1 yet, but will give it a go.
Thank you again.
Best wishes,
Lizzie
Thanks! I will try that - I have not used Gromacs 5.1 yet, but will give it a go.
Thank you again.
Best wishes,
Lizzie
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