[gmx-users] au virtual site

[fatemeh ramezani]

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?


ramezani