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 <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
========================================
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
