[gmx-users] water in lipid bilayer

N-J.M. Macaluso njmm2 at cam.ac.uk
Mon Nov 19 12:23:13 CET 2007

Thanks for your response,

I'm sorry, but I didn't find any text on the "membrane simulation" page on 
the wiki. What I meant by constraining waters in the z-direction is that at 
the start of the simulation, I constrained waters in the z-direction so 
that they wouldn't fall into the gap between the protein and membrane. In 
my case, the gap was large enough that some waters made their way in. I'm 
just wondering what I could do to make sure that the lipids aggregate 
around the protein properly. Should I manually delete these waters, or will 
the waters eventually make their way out during the course of the 

Many thanks,


On Nov 19 2007, Mark Abraham wrote:

>N-J.M. Macaluso wrote:
>> Hi,
>> I'm performing a transmembrane protein simulation in an explicit DPPC 
>> bilayer. I manually removed the lipids to accomodate my protein and the 
>> system has undergone 15 ns of equilibration.
>> In removing the lipids, I a gap betwteen the protein and membrane 
>> resulted. Most of the lipid molecules aggregated around the protein, but 
>> I have found that on one side of the protein, there are some water 
>> molecules that have found their way between the protein and lipid 
>> bilayer. Is there any way of removing these by altering the simulation 
>> parameters, or will I have to remove them manually? 
>See http://wiki.gromacs.org/index.php/Membrane_Simulations... these 
>waters may have been present in your initial structure.
>> I already 
>> constrained the waters in the z-direction at the start of the 
>> simulation, so that didn't work in this case.
>I don't understand this.
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