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

N-J.M. Macaluso njmm2 at cam.ac.uk
Tue Nov 6 15:11:47 CET 2007


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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