Molecular Dynamics of Protein-CNT(Carbon NanoTubes) Interaction
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I wish to enquire if there is a way to perform MD of Protein-CNT(Carbon NanoTubes) Interaction on SAMSON.
Thank you
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Dear @Ben,
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.
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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.
