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 <jalem...@vt.edu>
*À :* Discussion list for GROMACS users <gmx-users@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
========================================
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