[gmx-users] Re: Adding Ions

errabah fatima ezzahra errabahf at yahoo.fr
Wed Jul 13 21:13:35 CEST 2011

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.grothe  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??

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.


> 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:


All [moleculetype] names are available by default.  In your case you should probably just use "Protein Non-protein" as your tc-grps.


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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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