The 17-ala simulation was built initially to be used with a different integrator than the OpenMM one. As a consequence, the OpenMM integrator that is defined in the XML file, while it allows the simulation to run, does not introduce enough friction. This is especially noticeable as we do not have velocity reset (see #38 ). In conjunction with the large default force interval (see #171) , it makes tying a knot very difficult.
The 17-ala simulation was built initially to be used with a different integrator than the OpenMM one. As a consequence, the OpenMM integrator that is defined in the XML file, while it allows the simulation to run, does not introduce enough friction. This is especially noticeable as we do not have velocity reset (see #38 ). In conjunction with the large default force interval (see #171) , it makes tying a knot very difficult.