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 <[EMAIL PROTECTED]> 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 <[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 > > ****************************************** > > > > > > > > _______________________________________________ > 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
