I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing through [0,0,0] by and additional term to LJ potential in which the r=R-sqrt(x^2+y^2); R is the radius of a tube.
I want to simulate this system without pbc. Could you be so kind and give me advice which files of the source code should I modify? Thank you in advance.
Greetings
Zuzana
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