Hi Guys,

In the discussion at https://community.accelrys.com/message/8188#8188, it was mentioned to use a confined layer and constraints  to equilibrate a polymer. Can anyone maybe give me more details of this as I have a similar problem. I use a model of 6 polymer chains, each of 100 repeat units and wanted to relax the structure using Geometry optimization and NVT dynamics using Forcite. I also use obstacle molecules to avoid ring spearing and catenation, which I plan later to remove after slowly compressing the model to aravie at the experimental density. However, just after a few 100 ps the molecules start moving long distances and instead of being evenly distributed inside the amorphous cell, the polymer chains seem to cluster together forming areas of extremely high density and other regions of empty space as you can see in the attached picture.

Can someone maybe give me more details as to how I can use the confined layer and constraints to keep the chains and obstacle molecules confined to the amorphous cell to get a more evenly distributed model? I am unsure which atoms to actually select and to constrain, because I guess that another set of molecules and atoms will have to be selected after each cycle of optimization and dynamics calculation. Thus, can't one construct more than one confined layer so that the polymer is completely confined to the amorphous cell, upon which one can then perform a relaxation procedure?

I use MS 5.5 with Amorphous cell (the new version not the legacy version) and Forcite for optimization and dynamics calculations, all with the COMPASS forcefield. For dynamics calculations I am currently using the Andersen thermostat

Thank you very much

Dawie