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

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 29 00:50:57 CET 2011

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:


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