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 <[EMAIL PROTECTED]> > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Fwd: The question from the tutorial: Add water spc216.gro > (Tsjerk Wassenaar) > 2. problem with demo tutorial ([EMAIL PROTECTED]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Oct 2008 08:27:32 +0100 > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Subject: [gmx-users] Fwd: The question from the tutorial: Add water > spc216.gro > To: "Discussion list for GROMACS users" <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > 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 <[EMAIL PROTECTED]> > Date: Thu, Oct 30, 2008 at 7:35 AM > Subject: The question from the tutorial: Add water spc216.gro > To: Tsjerk Wassenaar <[EMAIL PROTECTED]> > > > 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: [EMAIL PROTECTED] > Subject: [gmx-users] problem with demo tutorial > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > 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" <[EMAIL PROTECTED]> > > Data: Mer, 29 Ottobre 2008, 7:29 pm > > A: "Discussion list for GROMACS users" <[email protected]> > > > -------------------------------------------------------------------------- > > > > 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:${PATH}" > > > > By the way, you can also use: > > > > source /usr/local/gromacs/bin/GMXRC > > > > which will set the PATH as well as some other relevant environment > > variables. > > > > Hope it helps, > > > > Tsjerk > > > > On Wed, Oct 29, 2008 at 6:52 PM, <[EMAIL PROTECTED]> wrote: > >> Hi! I installed GROMACS on my computer. I try to set up my environment > >> adding the line > >> > >> export PATH "/usr/local/gromacs/bin:${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 > >> > >> > >> > >> > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > >> posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > -- > > 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 [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 54, Issue 138 > ****************************************** >
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