Dear gromacs users,
I am working with a simulation of C60 fullerenes in water. One problem I faced is that during solvation step and subsequent steps of the MD, water molecules enter the fullerene cavity. Also I don’t want the fullerene molecule to change conformation, use it as a rigid body. For this purpose can I use the following two options:
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Add a virtual site at the center of the fullerene, give it a high sigma value, so that water will never enter the fullerene cavity; use constraints=all-bonds, so that the fullerene will not change conformation
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use three C-atoms of the fullerene to define 57 virtual sites; in that way conformation of the molecule will not change as well, use higher timesteps also
Let me know if the above two methods can be used or if any better method can be used.
Any help is much appreciated thank you