[gmx-users] problem with waters in protein/membrane simulation

Alan Dodd anoddlad at yahoo.com
Tue Nov 6 15:52:41 CET 2007

You can play with mdrun_hole (search the site) which is designed to create a protein-shaped hole in a lipid simulation (also making a hole in the water).
I'd probably just delete the offending waters, and reequilibrate, myself.

----- Original Message ----
From: N-J.M. Macaluso <njmm2 at cam.ac.uk>
To: gmx-users at gromacs.org
Sent: Tuesday, November 6, 2007 2:11:47 PM
Subject: [gmx-users] problem with waters in protein/membrane simulation


I'm having a small but significant problem with simulating a protein 
inserted in a DPPC membrane. I have simulated the system for 15 ns with 
position restraints on the protein to allow the lipids to anneal around it, 
but have recently found a small problem. I found a small gap between the 
protein and lipid where some water molecules embedded themselves. Is there 
any way I can change the parameters of the simulation to remove these 
waters, so that the lipids will aggregate properly around the protein? What 
would the best solution be? Should I just remove these waters manually?


Max Macaluso
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