[gmx-users] Re: Adding Ions

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> I am trying to do energy minimization but
> 
>     *
> 
> 
>                 grompp -f em.mdp -c waterbox_ions.gro -p file.top -o em.tpr
> 
>     *
> 
> 
>                 mdrun -v -s em.tpr -c system.gro
> 
> the  waterbox_ions.gro have the NA ions but when i check the system.gro 
> it does not have the ions
> 
> what am i doing wrong here??
> 

I see no possible way that mdrun could write an output configuration that 
deletes atoms from the input coordinates.  It violates the code.  How have you 
determined that the ions aren't there?  They're simply not in the .gro file or 
they're not showing up in some visualization software?

-Justin

> ------------------------------------------------------------------------
> *De :* Justin A. Lemkul <jalemkul at vt.edu>
> *À :* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Envoyé le :* Mercredi 13 Juillet 2011 14h42
> *Objet :* Re: Re : [gmx-users] Re: Adding Ions
> 
> 
> 
> errabah fatima ezzahra wrote:
>  >
>  > *I am trying to do a Short position restrained simulation so i wrote 
> * grompp -f pr.mdp -c system.gro -p file.top -o file.tpr , i added the 
> NA+ to the pr.mdp file
>  > here the pr.mdp
>  > tc-grps            =  Protein  W    NA+
> 
> First of all, you should never do this.
> 
> http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do
> 
>  > tau_t              =  0.1      0.1  0.1
>  > ref_t              =  300      300  300
>  > ; Energy monitoring
>  > energygrps          =  Protein  W    NA+
>  >
>  > but it gave me an error :
>  > Fatal error:
>  > Group NA+ not found in indexfile.
>  > Maybe you have non-default goups in your .mdp file, while not using 
> the '-n' option of grompp.
>  > In that case use the '-n' option.
>  > 
>  > i dont have an indexfile ?
> 
> The error message is a bit misleading.  I have changed it for the 
> upcoming release.  The group name "NA+" is incorrect in some way.  The 
> names you can specify in the .mdp file without creating an index group 
> are called "default groups," a listing of which (for version 4.5) can be 
> found at:
> 
> http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
> 
> All [moleculetype] names are available by default.  In your case you 
> should probably just use "Protein Non-protein" as your tc-grps.
> 
> -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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-- 
========================================

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

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