Dear all<br>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. <br>Can anybody please help me out?<br>Thanks in advance<br><br>Supti mukhopadhyay<br>
Phd student<br>NIMHANS <br>Bangalore<br><br><div class="gmail_quote">2008/10/30 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Fwd: The question from the tutorial: Add water spc216.gro<br>
(Tsjerk Wassenaar)<br>
2. problem with demo tutorial (<a href="mailto:cecilia.rosso@unito.it">cecilia.rosso@unito.it</a>)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 30 Oct 2008 08:27:32 +0100<br>
From: "Tsjerk Wassenaar" <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: [gmx-users] Fwd: The question from the tutorial: Add water<br>
spc216.gro<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:8ff898150810300027t7863d15s4f3f5f285b429a1d@mail.gmail.com">8ff898150810300027t7863d15s4f3f5f285b429a1d@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Lin,<br>
<br>
This is also gromacs related, rather than tutorial related. You<br>
followed the tutorial and now went off to try the procedures on your<br>
own system.<br>
<br>
As for the question, searching the user list with "settles" and<br>
"bounds" gives me the following:<br>
<a href="http://www.gromacs.org/pipermail/gmx-users/2007-March/026169.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2007-March/026169.html</a><br>
<br>
To me that's a rater "exact answer in the Archives of Gromacs".<br>
Apparently the spc.itp is included in the wrong place in your topology<br>
file. Time to read chapter 5 of the manual and get acquainted with the<br>
topology file format.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
---------- Forwarded message ----------<br>
From: Chih-Ying Lin <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>><br>
Date: Thu, Oct 30, 2008 at 7:35 AM<br>
Subject: The question from the tutorial: Add water spc216.gro<br>
To: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
<br>
<br>
Hi<br>
I have a molecule, which is not a protein.<br>
Then, I made a .top and a .gro file manually.<br>
And, I will like to see it in the water.<br>
<br>
<br>
<br>
I followed all the procedures I learned from the tutorials.<br>
The easiest way for me is to use all the commands and all of the .mdp<br>
files from the tutorials.<br>
<br>
<br>
But, I met the problem when I tried to add water into the system<br>
genbox -cp 1LW9-PBC.gro -cs spc216.gro -p 1LW9.top -o 1LW9-water.gro<br>
It showed :<br>
[ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:<br>
Atom index (1) in settles out of bounds (1-0)<br>
<br>
<br>
I could not find the exact answer in the Archives of Gromacs and it<br>
seems that everything is reasonable for me.<br>
<br>
Would you please instruct me what is the possible error I made?<br>
<br>
Thank you very much<br>
Lin<br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 30 Oct 2008 09:37:18 +0100 (CET)<br>
From: <a href="mailto:cecilia.rosso@unito.it">cecilia.rosso@unito.it</a><br>
Subject: [gmx-users] problem with demo tutorial<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:45548.130.192.200.144.1225355838.squirrel@mail.unito.it">45548.130.192.200.144.1225355838.squirrel@mail.unito.it</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
Hi Tsjerk!<br>
Thank you, now the shell works well!<br>
I have also the problem with the demo tutorial because when I tried to run<br>
the demo I received the next message<br>
<br>
demo: Command not found.<br>
<br>
Is there something to install to see the demo tutorial?<br>
Thanks,<br>
Cecilia<br>
<br>
><br>
><br>
> -------------------------- Messaggio originale ---------------------------<br>
> Oggetto: Re: [gmx-users] (no subject)<br>
> Da: "Tsjerk Wassenaar" <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
> Data: Mer, 29 Ottobre 2008, 7:29 pm<br>
> A: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> --------------------------------------------------------------------------<br>
><br>
> Hi Cecilia,<br>
><br>
> Please give your posts a descriptive title.<br>
> Then, this is actually a bash-related issue, which has not much to do<br>
> with Gromacs.<br>
> But then again, we're nice people :) The thing is that bash wants to have:<br>
><br>
> export PATH="/usr/local/gromacs/bin:${PATH}"<br>
><br>
> By the way, you can also use:<br>
><br>
> source /usr/local/gromacs/bin/GMXRC<br>
><br>
> which will set the PATH as well as some other relevant environment<br>
> variables.<br>
><br>
> Hope it helps,<br>
><br>
> Tsjerk<br>
><br>
> On Wed, Oct 29, 2008 at 6:52 PM, <<a href="mailto:cecilia.rosso@unito.it">cecilia.rosso@unito.it</a>> wrote:<br>
>> Hi! I installed GROMACS on my computer. I try to set up my environment<br>
>> adding the line<br>
>><br>
>> export PATH "/usr/local/gromacs/bin:${PATH}"<br>
>><br>
>> in the .bashrc file, but when I open my terminal, the next message<br>
>> appeared:<br>
>><br>
>> bash: export:<br>
>> `/usr/local/gromacs/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games':<br>
>> not a valid identifier<br>
>><br>
>> Why isn't it a valid identifier? What can I do?<br>
>><br>
>> The second problem is related to the demo tutorial: when I try to run<br>
>> the<br>
>> demo of the folder "tutor/gmxdemo" from the C shell the next message<br>
>> appeared:<br>
>><br>
>> demo: Command not found.<br>
>><br>
>> I don't know if these 2 problems are related each others or if they are<br>
>> not. Can you help me, please?<br>
>><br>
>> Thank you very much,<br>
>> Cecilia Rosso<br>
>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
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>><br>
><br>
><br>
><br>
> --<br>
> Tsjerk A. Wassenaar, Ph.D.<br>
> Junior UD (post-doc)<br>
> Biomolecular NMR, Bijvoet Center<br>
> Utrecht University<br>
> Padualaan 8<br>
> 3584 CH Utrecht<br>
> The Netherlands<br>
> P: +31-30-2539931<br>
> F: +31-30-2537623<br>
> _______________________________________________<br>
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><br>
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</blockquote></div><br><br clear="all"><br><br>