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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
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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 ([EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>)
----------------------------------------------------------------------
Message: 1
Date: Thu, 30 Oct 2008 08:27:32 +0100
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: [gmx-users] Fwd: The question from the tutorial: Add water
spc216.gro
To: "Discussion list for GROMACS users" <[email protected]
<mailto:[email protected]>>
Message-ID:
<[EMAIL PROTECTED]
<mailto:[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]
<mailto:[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] <mailto:[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] <mailto:[EMAIL PROTECTED]>
Subject: [gmx-users] problem with demo tutorial
To: [email protected] <mailto:[email protected]>
Message-ID: <[EMAIL PROTECTED]
<mailto:[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]
<mailto:[EMAIL PROTECTED]>>
> Data: Mer, 29 Ottobre 2008, 7:29 pm
> A: "Discussion list for GROMACS users"
<[email protected] <mailto:[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:${PATH}"
>
> By the way, you can also use:
>
> source /usr/local/gromacs/bin/GMXRC
>
> which will set the PATH as well as some other relevant environment
> variables.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Oct 29, 2008 at 6:52 PM, <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
>> Hi! I installed GROMACS on my computer. I try to set up my
environment
>> adding the line
>>
>> export PATH "/usr/local/gromacs/bin:${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
>>
>>
>>
>>
>> _______________________________________________
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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 [email protected]
<mailto:[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]
<mailto:[EMAIL PROTECTED]>.
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>
>
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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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