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DOPC Bilayer - Water Permeation
- robrob2013
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10 years 11 months ago - 10 years 11 months ago #1565
by robrob2013
DOPC Bilayer - Water Permeation was created by robrob2013
Dear all,
I would like to study the permeation of water in a DOPC bilayer assembly. I have read from other sources that in order to produce hydrostatic pressure differene in MD simulation, they have applied external forces on water molecules (along the +z direction). How would these things work on Martini? or what should I add on the mdp/top files? Is there any tutorial or references for this?
Again, thank you so much for all the help.
Cheers :)
Rob
I would like to study the permeation of water in a DOPC bilayer assembly. I have read from other sources that in order to produce hydrostatic pressure differene in MD simulation, they have applied external forces on water molecules (along the +z direction). How would these things work on Martini? or what should I add on the mdp/top files? Is there any tutorial or references for this?
Again, thank you so much for all the help.
Cheers :)
Rob
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- djurre
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10 years 11 months ago #1569
by djurre
Replied by djurre on topic DOPC Bilayer - Water Permeation
I'm not sure if this is what you mean, but you could use to pull code in Gromacs to pull a water molecule through a bilayer. In the Gromacs manual there is more explanation on how to use the pull code.
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- robrob2013
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10 years 11 months ago #1571
by robrob2013
Hi Djurre,
Again, thanks for the usual assistance. Sorry for the confusion. Let me clarify what I was trying to do. :)
I am considering a lipid bilayer assembly with water molecules on both sides.
I would like to investigate the water transport in a lipid bilayer under osmotic pressure difference. Is there a way which I can produce different pressure across the lipid bilayer using MARTINI model?
I've read in other MD simulations that they added external forces on the water molecules so as to produce pressure difference. Is this possible in the Martini model?
Any recommendation for this?
Thanks in advance. Cheers! :)
Rob
Replied by robrob2013 on topic DOPC Bilayer - Water Permeation
djurre wrote: I'm not sure if this is what you mean, but you could use to pull code in Gromacs to pull a water molecule through a bilayer. In the Gromacs manual there is more explanation on how to use the pull code.
Hi Djurre,
Again, thanks for the usual assistance. Sorry for the confusion. Let me clarify what I was trying to do. :)
I am considering a lipid bilayer assembly with water molecules on both sides.
I would like to investigate the water transport in a lipid bilayer under osmotic pressure difference. Is there a way which I can produce different pressure across the lipid bilayer using MARTINI model?
I've read in other MD simulations that they added external forces on the water molecules so as to produce pressure difference. Is this possible in the Martini model?
Any recommendation for this?
Thanks in advance. Cheers! :)
Rob
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- djurre
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10 years 11 months ago #1572
by djurre
Replied by djurre on topic DOPC Bilayer - Water Permeation
If people did it with other forcefields, I would expect it can be done with any (and thus Martini). But I've never done it.
To get a system with osmotic pressure over a bilayer, probably the easiest is to make a system with two parallel bilayers. You can then change the salt concentration in the intermembrane spaces.
Furthermore, the transport of water over bilayers might not be a very well reproduces phenomena. Check the literature (for example the polarizable water paper) for related information.
To get a system with osmotic pressure over a bilayer, probably the easiest is to make a system with two parallel bilayers. You can then change the salt concentration in the intermembrane spaces.
Furthermore, the transport of water over bilayers might not be a very well reproduces phenomena. Check the literature (for example the polarizable water paper) for related information.
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- robrob2013
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10 years 11 months ago #1573
by robrob2013
your a genius! thanks for the idea! :) :) :)
Replied by robrob2013 on topic DOPC Bilayer - Water Permeation
djurre wrote: To get a system with osmotic pressure over a bilayer, probably the easiest is to make a system with two parallel bilayers. You can then change the salt concentration in the intermembrane spaces.
your a genius! thanks for the idea! :) :) :)
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10 years 11 months ago #1583
by xavier
Oh yeaaaaa, Djurre he is good!
Replied by xavier on topic DOPC Bilayer - Water Permeation
robrob2013 wrote:
djurre wrote: To get a system with osmotic pressure over a bilayer, probably the easiest is to make a system with two parallel bilayers. You can then change the salt concentration in the intermembrane spaces.
your a genius! thanks for the idea! :) :) :)
Oh yeaaaaa, Djurre he is good!
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