Dear gromacs users I want to simulate gold nanoparticle by golp force field that needs to determine virtual sites for Au atoms. I read gromacs manual section 5.2.2 and 4.7 but it is not clear that how can I do it and .also I read virtual site tutorial for CO2 but it is for a 3 atomic molecule and I have a crystal by many atoms. I have a pdb file of my nanoparticle contain 600 atoms. How can specify their virtual site? Should I do it by hand? Do you know any command or software that can help me?
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