[gmx-users] Re: gmx-users Digest, Vol 54, Issue 138

Thu Oct 30 12:58:25 CET 2008

Hi Supti,

Subdivision is handled by mdrun. Just run grompp as it is.

And please do make a separate post with a descriptive title instead of
replying to a digest

Tsjerk

On 10/30/08, supti mukherjee <suptimukherjee at gmail.com> wrote:
> Dear all
> What is the command to run grompp in multiple processors in Gromacs version
> 4.0? It seems -np option does not work in Gromacs-4.0.
> Can anybody please help me out?
> Thanks in advance
>
> Supti mukhopadhyay
>  Phd student
> NIMHANS
> Bangalore
>
> 2008/10/30 <gmx-users-request at gromacs.org>
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> > Today's Topics:
> >
> >   1. Fwd: The question from the tutorial: Add water    spc216.gro
> >      (Tsjerk Wassenaar)
> >   2. problem with demo tutorial (cecilia.rosso at unito.it)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 30 Oct 2008 08:27:32 +0100
> > From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> > Subject: [gmx-users] Fwd: The question from the tutorial: Add water
> >        spc216.gro
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> >
> <8ff898150810300027t7863d15s4f3f5f285b429a1d at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi Lin,
> >
> > This is also gromacs related, rather than tutorial related. You
> > followed the tutorial and now went off to try the procedures on your
> > own system.
> >
> > As for the question, searching the user list with "settles" and
> > "bounds" gives me the following:
> >
> http://www.gromacs.org/pipermail/gmx-users/2007-March/026169.html
> >
> > To me that's a rater "exact answer in the Archives of Gromacs".
> > Apparently the spc.itp is included in the wrong place in your topology
> > file. Time to read chapter 5 of the manual and get acquainted with the
> > topology file format.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > ---------- Forwarded message ----------
> > From: Chih-Ying Lin <chihying2008 at gmail.com>
> > Date: Thu, Oct 30, 2008 at 7:35 AM
> > Subject: The question from the tutorial: Add water spc216.gro
> > To: Tsjerk Wassenaar <tsjerkw at gmail.com>
> >
> >
> > Hi
> > I have a molecule, which is not a protein.
> > Then, I made a .top and a .gro file manually.
> > And, I will like to see it in the water.
> >
> >
> >
> > I followed all the procedures I learned from the tutorials.
> > The easiest way for me is to use all the commands and all of the .mdp
> > files from the tutorials.
> >
> >
> > But, I met the problem when I tried to add water into the system
> > genbox -cp 1LW9-PBC.gro -cs spc216.gro -p 1LW9.top -o 1LW9-water.gro
> > It showed :
> > [ file "/usr/local/gromacs/share/gromacs/top/spc.itp",
> line 41 ]:
> >  Atom index (1) in settles out of bounds (1-0)
> >
> >
> > I could not find the exact answer in the Archives of Gromacs and it
> > seems that everything is reasonable for me.
> >
> > Would you please instruct me what is the possible error I made?
> >
> > Thank you very much
> > Lin
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 30 Oct 2008 09:37:18 +0100 (CET)
> > From: cecilia.rosso at unito.it
> > Subject: [gmx-users] problem with demo tutorial
> > To: gmx-users at gromacs.org
> > Message-ID:
> <45548.130.192.200.144.1225355838.squirrel at mail.unito.it>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Hi Tsjerk!
> > Thank you, now the shell works well!
> > I have also the problem with the demo tutorial because when I tried to run
> > the demo I received the next message
> >
> > demo: Command not found.
> >
> > Is there something to install to see the demo tutorial?
> > Thanks,
> > Cecilia
> >
> > >
> > >
> > > -------------------------- Messaggio originale
> ---------------------------
> > > Oggetto: Re: [gmx-users] (no subject)
> > > Da:      "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> > > Data:    Mer, 29 Ottobre 2008, 7:29 pm
> > > A:       "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > >
> --------------------------------------------------------------------------
> > >
> > > Hi Cecilia,
> > >
> > > Please give your posts a descriptive title.
> > > Then, this is actually a bash-related issue, which has not much to do
> > > with Gromacs.
> > > But then again, we're nice people :) The thing is that bash wants to
> have:
> > >
> > > export PATH="/usr/local/gromacs/bin:${PATH}"
> > >
> > > By the way, you can also use:
> > >
> > > source /usr/local/gromacs/bin/GMXRC
> > >
> > > which will set the PATH as well as some other relevant environment
> > > variables.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Wed, Oct 29, 2008 at 6:52 PM,  <cecilia.rosso at unito.it> wrote:
> > >> Hi! I installed GROMACS on my computer. I try to set up my environment
> > >> adding the line
> > >>
> > >> export PATH "/usr/local/gromacs/bin:${PATH}"
> > >>
> > >> in the .bashrc file, but when I open my terminal, the next message
> > >> appeared:
> > >>
> > >> bash: export:
> > >>
> `/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games':
> > >> not a valid identifier
> > >>
> > >> Why isn't it a valid identifier? What can I do?
> > >>
> > >> The second problem is related to the demo tutorial: when I try to run
> > >> the
> > >> demo of the folder "tutor/gmxdemo" from the C shell the next message
> > >> appeared:
> > >>
> > >> demo: Command not found.
> > >>
> > >> I don't know if these 2 problems are related each others or if they are
> > >> not. Can you help me, please?
> > >>
> > >> Thank you very much,
> > >> Cecilia Rosso
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
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> > >>
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > Junior UD (post-doc)
> > > Biomolecular NMR, Bijvoet Center
> > > Utrecht University
> > > Padualaan 8
> > > 3584 CH Utrecht
> > > The Netherlands
> > > P: +31-30-2539931
> > > F: +31-30-2537623
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
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> >
> >
> > ------------------------------
> >
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> > End of gmx-users Digest, Vol 54, Issue 138
> > ******************************************
> >
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623