[gmx-users] Changing temperature and pressure in lipid bilayer simulation.

[jhosamelly]

Thank you for your reply. I appreciate it. I'm reading the sections on the manual you said. I came across that before already but I don't really know how to apply it. LOL. I'll try to figure it out.

About the extraction of water from the bilayer. What I mean is, in a bilayer we know that the top part is water, the middle is the lipid and the bottom part is also water. What I wanna do is extract most of the water from the bilayer and the only thing left is the lipid (and maybe some water). Thanks.

Melsa Rose Ducut


> On Jan 24, 2014, at 8:07 AM, "Justin Lemkul [via GROMACS]" <ml-node+s5086n5013997h1 at n6.nabble.com> wrote:
> 
> 
> 
> On 1/23/14, 6:15 PM, jhosamelly wrote: 
> > So I did the martini tutorial in lipid bilayer. I now have a dspc lipid 
> > bilayer model. 
> > 
> > What I want to do is to change the temperature and pressure and see the 
> > effect of this on the dspc lipid bilayer. 
> > 
> > How should I do this?? Which part of the md.mdp file should I change? 
> > 
> 
> Manual sections 7.3.14 and 7.3.15 cover temperature and pressure coupling. 
> That's a good place to start. 
> 
> > Another question, what if I want to look for the pressure at which most of 
> > the water will be out of the bilayer. And I want to view the extraction of 
> > water from the bilayer. How should I do that? 
> > 
> 
> Isn't water normally excluded from the interior of the membrane?  Perhaps I 
> don't understand your question.  If you're trying to find the pressure at which 
> something happens, the most obvious approach is to systematically vary the 
> pressure until you observe the desired behavior. 
> 
> -Justin 
> 
> -- 
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> Justin A. Lemkul, Ph.D. 
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> 
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