[gmx-users] Re: Adding Ions

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> 
> you mean that i should have it as protein and Ions but no water
> 

No.  Please read what I said in the last message (it was likely exactly what you 
needed) and do some basic tutorial material if these concepts are unfamiliar to 
you.  You can't leave parts of your system untreated by the thermostat.  You'll 
get a fatal error if you try.

-Justin

> 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.
> 
> 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 
> <mailto: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 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

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

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

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