[gmx-users] Brownian Dynamics

[Michel N. Fodje]

Hi Everyone,

I a newbie in MD and gromacs.  I will like to do some brownian dynamics
simulation of a protein together with metal ions and I'm wondering if
any of you could help me out with some pointers. I've gone through the
tutorials and documentation and I'm having a problem determining:
	- How to specify the correct electrostatic model
	- if I should omit the solvent or not
	- How to obtain starting coordinates for the system, how far should the
ions be from the protein etc.
	- which parameters are important in the .mdp file appart from BD

Your help is highly appreciated,

Thanks,

Michel N. Fodje
Department of Molecular Biophysics,
Lund University - Sweden