[gmx-users] energy minimization of a charged system in vacuum

[Mark Abraham]

On 29/01/2011 9:57 AM, Matthew Chan wrote:
> Hi,
>
> I'm a first time GROMACS user. I've got 2 questions, which I'll ask in 
> separate emails. The first is about running EM on a charged protein in 
> vacuum.
>
> I'm presently walking through some of the tutorials and trying to 
> simplify them for my purposes. One is the energy minimization of the 
> 1AKI lysozyme protein. I would like to minimize this protein in vacuum 
> instead of solution as the tutorial demonstrates. Since the genion 
> program replaces water molecules with ions to balance the charge of 
> the system and there's no water, I'm having trouble running the 
> simulation with a neutral system.
>
> My question is what effect does running a simulation with a charged 
> system have? I recall reading that something related to PME 
> calculations assumes the system is neutral, but it did not specify 
> whether it was referring to MD or EM. From the mailing list, I have 
> only been able to determine that running a charged system in solution 
> makes no sense biologically.

Some threads elsewhere cover these issues:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html
http://archive.ambermd.org/200712/0223.html

Mark