[gmx-users] Polymer not diffusing into membrane

Alex s as1783 at hotmail.com
Tue Aug 12 07:15:20 CEST 2014

Dear Gromacs users
I'm not sure if this a question suitable for this forum but I would greatly appreciate it if you can help me in anyway regarding this issue.
I've have a system made up of a lipid bilayer, water and a single chain polymer.  My aim is to place the polymer just above the lipid bilayer in the water phase and let it diffuse into the bilayer. This polymer has been shown to interact with the lipid bilayer in previous studies us. The issue I'm having is that in my simulation the polymer stays in the water phase just hovering above the lipid membrane and never interacts or diffuses. I've tried simulating it in a number of different ways by varying the number of water molecules, changing box size or polymer position however I haven't had any success yet. The main steps in setting up my system is as follows:
1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the final box size of the lipid bilayer and use it to place the Polymer at specific point just above the lipid bilayer. 3. Perform energy minimization on the system4. Perform NVT and NPT5. Run the simulation
Any advice would be helpful

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