The polymer model with periodic boundary condition will cross the box wall. I want to build a polymer withnon-periodic boundary condition. How can I do?
Hope anyone’s kind response.
Are you intending to build only one polymer strand or multiple?
Thank you for your response.
I want to build 10 polymer chains and compact them into a box. Normally, periodic boundary condition will apply on three directions, i.e. x-y-z. However, I want to set non-periodic boundary condition on x direction. But some polymer chains crossing the box wall will break if the non-periodic boundary condition are forcibly applyed.
I don’t konw how to solve this problem.
Are you trying to build polymers between two walls? This would reflect their extensions back into the bulk. Or are you intending to build polymers, which extend into vacuum? This one could do by building a 3D bulk system and then increasing the box into e.g. the x direction. A trick could be to build two phases. The first phase would contain the polymer at condensed matter conditions, say at a density of 1 g/cc. The second phase could consist of water at very low density, say 0.001 g/cc. I would set option number to true. This allows you to specify the number of molecules when defining your clusters. Do you have a specific example of what you are trying to do?