[gmx-users] Fe(II) at active site

X.Periole X.Periole at rug.nl
Sat Jul 29 19:33:18 CEST 2006

> Well, you made a point of "Ions are big issue in MD 
>simulations". Could
> you please hint me what possible issues, so I can 
> search relavent to those keywords.

The main issue is the charge transfert which is not
possible to model with a basic MM force fields. Then
simulating a protein with an ions becomes an issue !

One reasonable think to do is to define convalent bonds
between the ions and the atoms interacting with it in
the protein. You won't see any change in the ion
coordination ... that should apply to your system.

Look the email list this issue was discussed many times.


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