errabah fatima ezzahra wrote:
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.gro
the 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??
I see no possible way that mdrun could write an output configuration that
deletes atoms from the input coordinates. It violates the code. How have you
determined that the ions aren't there? They're simply not in the .gro file or
they're not showing up in some visualization software?
-Justin
------------------------------------------------------------------------
*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
<mailto: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
<mailto:gmx-users-requ...@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
========================================
--
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
