[gmx-users] Polymer not diffusing into membrane

massimo sandal devicerandom at gmail.com
Tue Aug 12 10:41:56 CEST 2014

How long is your simulation? Are you sure it is long enough to see what you
want to see?
On 12 Aug 2014 07:15, "Alex s" <as1783 at hotmail.com> wrote:

> 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
> Regards
> Alex
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