[gmx-users] genion

[Justin A. Lemkul]

Eduardo Oliveira wrote:
> First, thanks for the help!
> 
> Yeah i chose System. But, regardless my wrong choice, I still want to 
> know why does the solvent group need to be a multiple pf 19 or whatever 
> number for that matter. I searched in the gmx-users mailling list and 
> noticed that this is a common occurance.
> 

What genion does is replace a continuous group of solvent molecules with ions. 
In order to do that, it needs to know how many atoms are in each solvent 
molecule.  In the case of water, the OW atom is replaced by the ion and the 
following 2 H atoms are deleted, because genion detects that water has 3 atoms. 
  In your case, whatever the first molecule in your system is has 19 atoms, and 
thus genion assumes that the remaining molecules in the group "System" are each 
composed of 19 atoms.  When it finds that this is not the case, it triggers a 
fatal error, rather than merrily deleting 19 atoms at a time to give a horribly 
fragmented, completely useless system.

-Justin

> 
> 
> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Eduardo Oliveira <eduardobio at yahoo.com.br>; Discussion list for 
> GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Sábado, 31 de Março de 2012 14:25
> *Assunto:* Re: [gmx-users] genion
> 
> 
> 
> Eduardo Oliveira wrote:
>  > Hi all,
>  >
>  > I' ve stumbled upon a problem when i used genion to prepare my files. 
> Here's the comand line:
>  >
>  > genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq 
> -1 -p sistema.toI
>  >
>  > I've got this in return:
>  >
>  > Fatal error:
>  > Your solvent group size (73282) is not a multiple of 19.
>  >
> 
> What did you choose as the group in which to insert ions?  If you chose 
> "System," that's an incorrect approach.  I would suggest you refer to to 
> some basic tutorial material to make these workflows more clear.
> 
> http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================