[gmx-users] the reson for neutralizing the charge

[Mark Abraham]

Homa Azizian wrote:
> Hi 
> I have a basic question about the charge. why is it important to neutralize 
> the charge of ligand-protein complex. Is it true by neutralizing the tatal 
> charge of ligand-protein complex we prevent the electrostatic intraction of 
> ligand and protein?
> Any suggestion would be appreciated.

Physical systems are normally neutral - cells have to do work to 
maintain ion and/or charge imbalances.

Physical models were normally parameterized under neutral conditions - 
but you should check the literature for your force field.

Some algorithms might be doubtful under non-neutral conditions - I'm not 
sure whether Ewald methods are well-formed in such cases. Most 
derivations I've seen seem to require it.

Mark