[gmx-users] Simulations enclosed in sphere and arbitrary defined non standard interactions

Michał Kadlof m.kadlof at cent.uw.edu.pl
Tue Apr 5 15:33:55 CEST 2016


I would like to run my simulations inside closed sphere. It may be something like soft-walls potential (0 inside a sphere, and proportional to r^2 outside sphere with force directed to the center of sphere) or something similar. Is it possible with Gromacs? I'm not afraid to mess up with a Gromacs code a little bit if it necessary.

I'm also curious if it possible to add harmonic interaction between arbitrary chosen two beads in simulations. I would also like to define different interaction constant for each such spring separately.

Michał Kadlof

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