[gmx-users] au virtual site

Justin Lemkul jalemkul at vt.edu
Mon Sep 3 01:54:56 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list