Molecular Dynamics of Protein-CNT(Carbon NanoTubes) Interaction
I wish to enquire if there is a way to perform MD of Protein-CNT(Carbon NanoTubes) Interaction on SAMSON.
For simple minimization of protein-CNT, you can use Universal Force Field in SAMSON, but it will not be suitable for MD simulation. You can try using the Gromacs Wizard module for simulation of protein-CNT interactions. See e.g. this tutorial from Gromacs: Gromacs How-To: Carbon Nanotube. But it describes only CNT simulation. As for the simulation of protein-CNT interaction you might need to check which force field to use and maybe modify some FF parameters.
Indeed in the current version of the Gromacs Wizard, you will need to have a force field which allows for both biomolecules and CNTs. Then you can add such a force field in the settings of the module. However using a 'one-shot parameterization' (e.g. using the ATB server) will not work at the moment with the Gromacs Wizard.