[gmx-users] keeping water (entirely) out of the bilayer core

[Christopher Neale]

Thank you for the advice Jianguo. This seems like a good way forward. I was hoping not to have to learn how to use new software, but perhaps it is time.

Thank you,
Chris.


-- original message --

Hi Chris,

Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective variable as 
mindist between the water molecules and the lipid tails. And then apply wall potential to keep 
this CV above a certain value. 

Jianguo 

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Dear users:

I am interested in running simulations of lipid bilayers in which I keep all water molecules out of
the bilayer core(not just statistically, but absolutely). However, I have been unable to figure out
how to do it. I'll list what I have tried in the hope that others have some ideas or even perhaps 
know how to do this with standard gromacs.
...