[gmx-users] virtual sites

[Mark Abraham]

zhang wrote:
> Dear users,
>      I use the Cationic Dummy Atom methods by Pang to simulate a protein 
> containing Zn2+. How to get the parameters in [ virtual_sites? ] 
> section? I use the model  4fd.
>      In the following example, how to get the value of parameters a, b 
> and d?
> 
>        [ virtual sites4 ]
> 
>        ; Site from funct a b d
> 
>        5 1 2 3 4 1 0.33333 0.33333 -0.105
> 
>          Thanks in advance!

Have you read the manual section on virtual sites, and consulted the 
part of manual chapter 5 to see how this part might work?

Mark