[gmx-users] Re: Adding Ions
errabah fatima ezzahra
errabahf at yahoo.fr
Wed Jul 13 22:19:15 CEST 2011
you mean that i should have it as protein and Ions but no water
tc-grps = Protein ions
tau_t = 0.1 0.1
ref_t = 300 300
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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