[gmx-users] au virtual site

[Justin Lemkul]

On 9/1/12 3:38 PM, fatemeh ramezani wrote:
>
> 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?
>

You'll have to define how the virtual sites need to be constructed.  There are 
many ways to do so.  See manual section 4.7, especially Figure 4.16.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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