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

Jianguo Li ljggmx at yahoo.com.sg
Tue May 7 03:59:08 CEST 2013

Hi Chris, 

Just think of another possible way without modifying the code. The task can be achieved by increasing the LJ repulsion term between the lipid tail atoms and water molecules, but keeping all other interactions unchanged. To do so, the free energy code can be used. You can create a state_B, at which only the LJ repulsion term between the lipid tail atoms and water molecules is rescaled, other interactions are the same as state_A, and then run the simulations at lambda=1. 


 From: Christopher Neale <chris.neale at mail.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
Sent: Monday, 6 May 2013, 2:46
Subject: [gmx-users] keeping water (entirely) out of the bilayer core

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,

-- 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. 



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.
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