[gmx-users] Re: gmx-users Digest, Vol 54, Issue 138
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 30 12:55:24 CET 2008
supti mukherjee 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?
You don't need to specify -np with grompp anymore.
-Justin
> Thanks in advance
>
> Supti mukhopadhyay
> Phd student
> NIMHANS
> Bangalore
>
> 2008/10/30 <gmx-users-request at gromacs.org
> <mailto: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
> <mailto:cecilia.rosso at unito.it>)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Oct 2008 08:27:32 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <8ff898150810300027t7863d15s4f3f5f285b429a1d at mail.gmail.com
> <mailto: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
> <mailto: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 <mailto: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 <mailto:cecilia.rosso at unito.it>
> Subject: [gmx-users] problem with demo tutorial
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID: <45548.130.192.200.144.1225355838.squirrel at mail.unito.it
> <mailto: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
> <mailto:tsjerkw at gmail.com>>
> > Data: Mer, 29 Ottobre 2008, 7:29 pm
> > A: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org <mailto: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:${PATH}"
> >
> > By the way, you can also use:
> >
> > source /usr/local/gromacs/bin/GMXRC
> >
> > which will set the PATH as well as some other relevant environment
> > variables.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Wed, Oct 29, 2008 at 6:52 PM, <cecilia.rosso at unito.it
> <mailto:cecilia.rosso at unito.it>> wrote:
> >> Hi! I installed GROMACS on my computer. I try to set up my
> environment
> >> adding the line
> >>
> >> export PATH "/usr/local/gromacs/bin:${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
> <mailto:gmx-users at gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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>
>
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> End of gmx-users Digest, Vol 54, Issue 138
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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