[gmx-users] the reson for neutralizing the charge

Berk Hess gmx3 at hotmail.com
Tue Apr 7 09:46:29 CEST 2009


The issue here is not so much net neutrality of the whole system
(although there can be important reasons for wanted this),
but that your system has a small fractional charge.
This indicates that there a probably missing atoms, probably in your ligand.
That is a serious problem which you should fix.
Check if all atoms in your ligand are present in the topology file.


> Date: Tue, 7 Apr 2009 17:16:19 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] the reson for neutralizing the charge
> 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
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