[gmx-users] Addition of ions in vacuum simulations

[David van der Spoel]

OZGE ENGIN wrote:
> Hi Mark,
> 
> I think, it is not a chemistry question exactly. 
> Genion command asks for a group whose atoms are replaced with ions.
> I have no solvent molecules in my system. 
> In this respect, how can I incorporate ions into my system? 
> 
use a text editor.

> Thanks
> 
> Ozge
> 
> -----Original Message-----
> From: "Mark Abraham" <mark.abraham at anu.edu.au>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thu, 18 Oct 2007 16:49:15 +1000 (EST)
> Subject: Re: [gmx-users] Addition of ions in vacuum simulations
> 
>> Hi all,
>>
>> I am simulating a charged peptide in vacuum. I want to neutralize my
>> system by using genion command,and as expected it asks me a continuous
>> solvent group for the replacement; however, I have no solvents.
>>
>> How can I add ions to my system if I am in vacuum? or Is it necessary to
>> add ions while performing simulations in vacuum?
> 
> This is a chemistry question that will depend on your protein and what
> you're trying to study. In some cases you might also consider modifying
> the chemical groups so that there is not an ion there.
> 
> Mark
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se