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Zero Surface Tension
- sdf
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13 years 2 months ago #521
by sdf
Zero Surface Tension was created by sdf
I just want to make sure I am getting this. When I read papers on lipid bilayers, they often simulate at "zero surface tension". For this, I have been using
Pcoupltype = semiisotropic
ref_p = 0.0 1.0
because the GROMACS manual says that
"""The first ref_p value is the reference surface tension times the number of surfaces [bar nm], the second value is the reference z-pressure [bar]"""
However, after seeing the standard MARTINI mdp options file...
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
I am beginning to wonder if I should simulate zero surface tension with pressure coupled separately at 1.0 bar in each direction.
So, can someone please confirm that I should be using
Pcoupletype = semiisotropic
ref_p = 1.0 1.0
and maybe explain why you wouldn't use 0.0 for the first coupling value.
Also, while I am at it, is there any difference between Pcoupletype "semiisotropic" and "surface-tension?"
Thank you for any help.
Pcoupltype = semiisotropic
ref_p = 0.0 1.0
because the GROMACS manual says that
"""The first ref_p value is the reference surface tension times the number of surfaces [bar nm], the second value is the reference z-pressure [bar]"""
However, after seeing the standard MARTINI mdp options file...
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
I am beginning to wonder if I should simulate zero surface tension with pressure coupled separately at 1.0 bar in each direction.
So, can someone please confirm that I should be using
Pcoupletype = semiisotropic
ref_p = 1.0 1.0
and maybe explain why you wouldn't use 0.0 for the first coupling value.
Also, while I am at it, is there any difference between Pcoupletype "semiisotropic" and "surface-tension?"
Thank you for any help.
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- xavier
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13 years 2 months ago #568
by xavier
Thank you for any help.[/quote]
Replied by xavier on topic Zero Surface Tension
This would have you to simulate a system with a zero pressure on the x/y plane!sdf wrote: I just want to make sure I am getting this. When I read papers on lipid bilayers, they often simulate at "zero surface tension". For this, I have been using
Pcoupltype = semiisotropic
ref_p = 0.0 1.0
gromacs says this indeed but in the section "surface-tension" of the pressure coupling options.because the GROMACS manual says that
"""The first ref_p value is the reference surface tension times the number of surfaces [bar nm], the second value is the reference z-pressure [bar]"""
I believe you should read the pressure control in the gromacs manual.
However, after seeing the standard MARTINI mdp options file...
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
I am beginning to wonder if I should simulate zero surface tension with pressure coupled separately at 1.0 bar in each direction.
So, can someone please confirm that I should be using
Pcoupletype = semiisotropic
ref_p = 1.0 1.0
and maybe explain why you wouldn't use 0.0 for the first coupling value.
Also, while I am at it, is there any difference between Pcoupletype "semiisotropic" and "surface-tension?"
Thank you for any help.[/quote]
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- sdf
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13 years 2 months ago #601
by sdf
Replied by sdf on topic Zero Surface Tension
You are completely right. I dont know why, but I guess the two pressure options caught me off guard. Turns out that I was specifying the correct pressure though. Thanks for helping get that cleared up.
Now, if I can only nail down the compressibility issue...
md.chem.rug.nl/cgmartini/index.php/user-...rm/forum/topic?id=62
Now, if I can only nail down the compressibility issue...
md.chem.rug.nl/cgmartini/index.php/user-...rm/forum/topic?id=62
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