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comperssibility in coarse grained lipid bilayer
- yamahdi
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13 years 2 months ago #523
by yamahdi
comperssibility in coarse grained lipid bilayer was created by yamahdi
Hi,
would you please help me explaining if there is any rule for defining comperssibility in coarse grained lipid bilayer models?
thanks in advance
would you please help me explaining if there is any rule for defining comperssibility in coarse grained lipid bilayer models?
thanks in advance
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- xavier
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13 years 2 months ago #527
by xavier
In the Martini force field simulation a compressibility of 4.5E-5 is used for all type of systems. It corresponds to the experimental water compressibility (see ref marring-JPC/B-2004) and allows to reproduce most of experimental values for a set of liquid and membrane phases (same reference).
XAvier.
Replied by xavier on topic comperssibility in coarse grained lipid bilayer
yamahdi wrote: Hi,
would you please help me explaining if there is any rule for defining comperssibility in coarse grained lipid bilayer models?
thanks in advance
In the Martini force field simulation a compressibility of 4.5E-5 is used for all type of systems. It corresponds to the experimental water compressibility (see ref marring-JPC/B-2004) and allows to reproduce most of experimental values for a set of liquid and membrane phases (same reference).
XAvier.
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13 years 2 months ago #534
by yamahdi
Replied by yamahdi on topic comperssibility in coarse grained lipid bilayer
Hi
thanks for your kind help
thanks for your kind help
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13 years 2 months ago #578
by yamahdi
Replied by yamahdi on topic comperssibility in coarse grained lipid bilayer
Hi every body
first we had simulated system of POPC and a protein with tow different comperssibility, then we have modified the comperssibility and used 4.4E-5 and repeat the simulation, also we did another simuliestion with comperssibility of 1E-5 but in all of these three cases we have had a same problem: the simulation box has been streched in z direction!!! the changes in compressibility have not had any effect on the result! I should mention that duration of simulation had been 25 ns.
would you polease help me explainig where may had been my mistake?
thanks for your kind help in advance
first we had simulated system of POPC and a protein with tow different comperssibility, then we have modified the comperssibility and used 4.4E-5 and repeat the simulation, also we did another simuliestion with comperssibility of 1E-5 but in all of these three cases we have had a same problem: the simulation box has been streched in z direction!!! the changes in compressibility have not had any effect on the result! I should mention that duration of simulation had been 25 ns.
would you polease help me explainig where may had been my mistake?
thanks for your kind help in advance
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13 years 2 months ago #600
by sdf
Xavier: Are you sure? In the "STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1" it suggests a compressibility of 3E-4.
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
The FAQ page, where this file comes from says that it was last updated May 2010.
md.chem.rug.nl/cgmartini/index.php/downl.../54-input-parameters
The paper you referenced was only Martini 1.0, published in 2004. And it only references an old website. So, why are you using 4.5E-5? I only ask because this is an issue I am trying to clear up as well.
Replied by sdf on topic comperssibility in coarse grained lipid bilayer
xavier wrote:
yamahdi wrote: Hi,
would you please help me explaining if there is any rule for defining comperssibility in coarse grained lipid bilayer models?
thanks in advance
In the Martini force field simulation a compressibility of 4.5E-5 is used for all type of systems. It corresponds to the experimental water compressibility (see ref marring-JPC/B-2004) and allows to reproduce most of experimental values for a set of liquid and membrane phases (same reference).
XAvier.
Xavier: Are you sure? In the "STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1" it suggests a compressibility of 3E-4.
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
The FAQ page, where this file comes from says that it was last updated May 2010.
md.chem.rug.nl/cgmartini/index.php/downl.../54-input-parameters
The paper you referenced was only Martini 1.0, published in 2004. And it only references an old website. So, why are you using 4.5E-5? I only ask because this is an issue I am trying to clear up as well.
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13 years 2 months ago #605
by xavier
Ok, you are right. The value most commonly used is the 3E-4.
What is important to consider relatively to pressure coupling are the following points:
1- the change of compressibility from 4E-5 to 3E-4 in the mdp file is not expected to affect the actual compressibility of the system in a significant manner.
2- What matters more is the ratio of the coupling parameter (tau_p) and the compressibility. They actually appear like that in the pressure control of the Berendsen thermostat.
3- The actual compressibility of the system is determined from the fluctuations of the volume.
I hope this answers your concerns.
XAvier.
Replied by xavier on topic comperssibility in coarse grained lipid bilayer
sdf wrote:
xavier wrote:
yamahdi wrote: Hi,
would you please help me explaining if there is any rule for defining comperssibility in coarse grained lipid bilayer models?
thanks in advance
In the Martini force field simulation a compressibility of 4.5E-5 is used for all type of systems. It corresponds to the experimental water compressibility (see ref marring-JPC/B-2004) and allows to reproduce most of experimental values for a set of liquid and membrane phases (same reference).
XAvier.
Xavier: Are you sure? In the "STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1" it suggests a compressibility of 3E-4.
md.chem.rug.nl/cgmartini/images/paramete...ini_v2.x_example.mdp
The FAQ page, where this file comes from says that it was last updated May 2010.
md.chem.rug.nl/cgmartini/index.php/downl.../54-input-parameters
The paper you referenced was only Martini 1.0, published in 2004. And it only references an old website. So, why are you using 4.5E-5? I only ask because this is an issue I am trying to clear up as well.
Ok, you are right. The value most commonly used is the 3E-4.
What is important to consider relatively to pressure coupling are the following points:
1- the change of compressibility from 4E-5 to 3E-4 in the mdp file is not expected to affect the actual compressibility of the system in a significant manner.
2- What matters more is the ratio of the coupling parameter (tau_p) and the compressibility. They actually appear like that in the pressure control of the Berendsen thermostat.
3- The actual compressibility of the system is determined from the fluctuations of the volume.
I hope this answers your concerns.
XAvier.
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13 years 2 months ago #611
by sdf
This is another question I have. When I try to configure(grompp) with tau_p=1.0 and compressibility=3E-4 as suggested in the standard mdp file
md.chem.rug.nl/cgmartini/index.php/downl.../54-input-parameters
I get a warning that says tau_p should be atleast 2 orders of magnitude greater than the timestep for proper pressure coupling. The timestep in that file is 0.04. (I actually use 0.02). But why are these parameters suggested if they do not give proper pressure coupling? Should I just ignore the warning? When I do, everything seems to run fine. Or, scale up compressibility and tau_p together to maintain the same ratio but achieve tau_p two orders of magnitude greater than the timestep. Thanks
Replied by sdf on topic comperssibility in coarse grained lipid bilayer
xavier wrote: 2- What matters more is the ratio of the coupling parameter (tau_p) and the compressibility. They actually appear like that in the pressure control of the Berendsen thermostat.
This is another question I have. When I try to configure(grompp) with tau_p=1.0 and compressibility=3E-4 as suggested in the standard mdp file
md.chem.rug.nl/cgmartini/index.php/downl.../54-input-parameters
I get a warning that says tau_p should be atleast 2 orders of magnitude greater than the timestep for proper pressure coupling. The timestep in that file is 0.04. (I actually use 0.02). But why are these parameters suggested if they do not give proper pressure coupling? Should I just ignore the warning? When I do, everything seems to run fine. Or, scale up compressibility and tau_p together to maintain the same ratio but achieve tau_p two orders of magnitude greater than the timestep. Thanks
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13 years 1 month ago #612
by yamahdi
Replied by yamahdi on topic comperssibility in coarse grained lipid bilayer
Hi
I should mention that we have solved the warnings about the ratio of tau_p and time step and after all we have had the problem with comperssibility! water molecules are coming toward up and down of the simulation box and the area of simulation box in xy is reducing and the height in z direction in incrising.I think using a bigger compersibillity will lead in more critical situation. would you please help me?
thsnks for your kind help in advance
I should mention that we have solved the warnings about the ratio of tau_p and time step and after all we have had the problem with comperssibility! water molecules are coming toward up and down of the simulation box and the area of simulation box in xy is reducing and the height in z direction in incrising.I think using a bigger compersibillity will lead in more critical situation. would you please help me?
thsnks for your kind help in advance
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13 years 1 month ago #613
by xavier
Ok, the compressibility in the mdp file has no real physical meaning. I mean that it is present in the pressure control and is indeed the compressibility of the system but it will not be the actual compressibility of the system.
I would suggest that you keep the original 3E-4 and modify tau_p to 5 ps. 1 ps is actually a bit tight. That should get ride of the warnings and are reasonable parameters.
If the parameters give warning it is likely because they have been developed and used with an earlier version of GMX in which the warning were not given. These warnings are only warning and mostly there to avoid a non-experimented user to make important mistakes. The set-ups files given in the web-site are fine and have been extensively used.
In your case it would be interesting to understand what is happening. Try top use the files given in the website and see what happens then. Your system might experience a liquid to liquid-ordered transition.
Replied by xavier on topic comperssibility in coarse grained lipid bilayer
yamahdi wrote: Hi
I should mention that we have solved the warnings about the ratio of tau_p and time step and after all we have had the problem with comperssibility! water molecules are coming toward up and down of the simulation box and the area of simulation box in xy is reducing and the height in z direction in incrising.I think using a bigger compersibillity will lead in more critical situation. would you please help me?
thsnks for your kind help in advance
Ok, the compressibility in the mdp file has no real physical meaning. I mean that it is present in the pressure control and is indeed the compressibility of the system but it will not be the actual compressibility of the system.
I would suggest that you keep the original 3E-4 and modify tau_p to 5 ps. 1 ps is actually a bit tight. That should get ride of the warnings and are reasonable parameters.
If the parameters give warning it is likely because they have been developed and used with an earlier version of GMX in which the warning were not given. These warnings are only warning and mostly there to avoid a non-experimented user to make important mistakes. The set-ups files given in the web-site are fine and have been extensively used.
In your case it would be interesting to understand what is happening. Try top use the files given in the website and see what happens then. Your system might experience a liquid to liquid-ordered transition.
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13 years 1 month ago #614
by xavier
Replied by xavier on topic comperssibility in coarse grained lipid bilayer
One last comment. The warnings in GMX most often assume that you are running a atomistic system and the "rules" might not strictly apply to CG models and in particular to MARTINI.
You may ignore the warning given by grompp!
XAvier
You may ignore the warning given by grompp!
XAvier
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