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 <[email protected]>
*Para:* Eduardo Oliveira <[email protected]>; Discussion list for
GROMACS users <[email protected]>
*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
========================================
--
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