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procedure to obtain self-assembled patches larger than 128 lipids
- mferraro
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11 years 1 month ago #1475
by mferraro
procedure to obtain self-assembled patches larger than 128 lipids was created by mferraro
Hi,
I'm trying to generate a self-assembled membrane system containing approximately 420 DSPC molecules. I've already read the two topics about this issues but none of them satisfies my question. I made the 128 DSPC tutorial and it works fine, but when I adapted this system to my box I have micellas instead of bilayers. I tried to run multiple simulations with "gen_vel = yes" but the result has not changed. Is it reasonable to generate a self-assembled membrane for systems with a greater number of lipids or maybe do I have to work on a smaller patch (128) and then multiply this according to my needs? This issue seems not clear from previous topics.
I use this opportunity also to deal with the flag "gen_vel" in mdp files downloaded from tutorial page. This option is turned OFF (no) even if we use this md.mdp file as the input for self-assembly after having done the minimization. But at the end of minimization we don't have velocities, so in this option is turned off, where does the integrator in md-steps take the informatuion about them? Am I wrong?
I will be so much grateful to anyone who could please give me any information about that.
I'm trying to generate a self-assembled membrane system containing approximately 420 DSPC molecules. I've already read the two topics about this issues but none of them satisfies my question. I made the 128 DSPC tutorial and it works fine, but when I adapted this system to my box I have micellas instead of bilayers. I tried to run multiple simulations with "gen_vel = yes" but the result has not changed. Is it reasonable to generate a self-assembled membrane for systems with a greater number of lipids or maybe do I have to work on a smaller patch (128) and then multiply this according to my needs? This issue seems not clear from previous topics.
I use this opportunity also to deal with the flag "gen_vel" in mdp files downloaded from tutorial page. This option is turned OFF (no) even if we use this md.mdp file as the input for self-assembly after having done the minimization. But at the end of minimization we don't have velocities, so in this option is turned off, where does the integrator in md-steps take the informatuion about them? Am I wrong?
I will be so much grateful to anyone who could please give me any information about that.
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- xavier
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11 years 1 month ago #1478
by xavier
Replied by xavier on topic procedure to obtain self-assembled patches larger than 128 lipids
I would guess that the formation of micelle/bilayer would be function of the lipid/water ratio or hydration level of the lipids.
In your case it is not clear what hydration level you have but if you aim is not the study of the mechanism of bilayer formation I would suggest you use a smaller box and then replicate it to reach the box size you need.
In your case it is not clear what hydration level you have but if you aim is not the study of the mechanism of bilayer formation I would suggest you use a smaller box and then replicate it to reach the box size you need.
mferraro wrote: Hi,
I'm trying to generate a self-assembled membrane system containing approximately 420 DSPC molecules. I've already read the two topics about this issues but none of them satisfies my question. I made the 128 DSPC tutorial and it works fine, but when I adapted this system to my box I have micellas instead of bilayers. I tried to run multiple simulations with "gen_vel = yes" but the result has not changed. Is it reasonable to generate a self-assembled membrane for systems with a greater number of lipids or maybe do I have to work on a smaller patch (128) and then multiply this according to my needs? This issue seems not clear from previous topics.
I use this opportunity also to deal with the flag "gen_vel" in mdp files downloaded from tutorial page. This option is turned OFF (no) even if we use this md.mdp file as the input for self-assembly after having done the minimization. But at the end of minimization we don't have velocities, so in this option is turned off, where does the integrator in md-steps take the informatuion about them? Am I wrong?
I will be so much grateful to anyone who could please give me any information about that.
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- mferraro
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11 years 4 weeks ago #1479
by mferraro
Replied by mferraro on topic procedure to obtain self-assembled patches larger than 128 lipids
Dear Xavier,
thanks a lot for your precious reply.
I obtained my bilayer!! :D
Anyway you don't say anything about velocities. Do I have to turn the flag gen_vel to "yes" in md.mdp file or not?
And finally, now that I've my bilayer at 323 Kelvin, could I have any problems in cooling the system to 298 Kelvin? I would like to simulate it at physiological temperature changing the nature of lipids (raft-like); I am not sure if it is better to make the change at 323, equilibrate and then cool the mixed bilayer at 298, or directly run my self-assembly at 298 K and at the end change lipids at my target temperature.
Any suggestion will be very appreciated.
Grateful in advance.
thanks a lot for your precious reply.
I obtained my bilayer!! :D
Anyway you don't say anything about velocities. Do I have to turn the flag gen_vel to "yes" in md.mdp file or not?
And finally, now that I've my bilayer at 323 Kelvin, could I have any problems in cooling the system to 298 Kelvin? I would like to simulate it at physiological temperature changing the nature of lipids (raft-like); I am not sure if it is better to make the change at 323, equilibrate and then cool the mixed bilayer at 298, or directly run my self-assembly at 298 K and at the end change lipids at my target temperature.
Any suggestion will be very appreciated.
Grateful in advance.
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- xavier
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11 years 3 weeks ago #1488
by xavier
Replied by xavier on topic procedure to obtain self-assembled patches larger than 128 lipids
Good you obtained your bilayer.
I do not think that the initial set of velocities will have an impact on the simulation.
You can cool down your already formed bilayer, no problem but be careful not to go too low in temperature. Your bilayer might freeze. Check the transition temperature of your lipid.
I do not think that the initial set of velocities will have an impact on the simulation.
You can cool down your already formed bilayer, no problem but be careful not to go too low in temperature. Your bilayer might freeze. Check the transition temperature of your lipid.
mferraro wrote: Dear Xavier,
thanks a lot for your precious reply.
I obtained my bilayer!! :D
Anyway you don't say anything about velocities. Do I have to turn the flag gen_vel to "yes" in md.mdp file or not?
And finally, now that I've my bilayer at 323 Kelvin, could I have any problems in cooling the system to 298 Kelvin? I would like to simulate it at physiological temperature changing the nature of lipids (raft-like); I am not sure if it is better to make the change at 323, equilibrate and then cool the mixed bilayer at 298, or directly run my self-assembly at 298 K and at the end change lipids at my target temperature.
Any suggestion will be very appreciated.
Grateful in advance.
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