[gmx-users] Re: Adding Ions

[errabah fatima ezzahra]

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.

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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110713/174beae7/attachment.html>