[gmx-users] interaction with metal

[Justin Lemkul]

On 3/21/13 8:59 PM, Nur Syafiqah Abdul Ghani wrote:
> Hi guys,
>
> I have a question..Regarding to my project,i want to make a simulation
> between metal and my protein in mix solvent condition.
>
> BUt for gromacs,at the genion part can i run it for two times?
> First to make my simulation system is neutral and the second one is to
> use the genion to put the metal and interact it with my protein.Is it
> possible to do that?
>

genion only inserts ions randomly, so if you need to specify a particular 
location for your metal ion, you're better off simply setting its coordinates 
with e.g. editconf and placing it in your box, then adding solvent and whatever 
other ions you need.

-Justin

-- 
========================================

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

========================================