[gmx-users] virtual site of Au crystal

fatemeh ramezani fr_750 at yahoo.com
Tue Aug 28 22:58:43 CEST 2012

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?

many thanks


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