pycgtool (conda): PyCGTOOL is a tool to aid in parametrising coarse-grained (CG) molecular mechanics models of small molecules, for example for simulations using the popular MARTINI model. It generates coarse-grained model parameters from atomistic simulation trajectories using a user-provided mapping. Equilibrium values and force constants of bonded terms are calculated by Boltzmann Inversion of bond distributions collected from the input trajectory.
Keywords: coarse-grained-molecular-dynamics|computational-chemistry|gromacs|molecular-dynamics|python|science