Okay, thanks. I will install it again in some other directory.
Majid
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Gromacs Users' List <gmx-users@gromacs.org>
Sent: Sun, February 13, 2011 1:39:16 PM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan wrote:
> Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs
now.
>
You normally don't want to do any work within the Gromacs installation
directories. For the demo, I suppose it's alright, but sudo is really just a
work-around to write in directories which normally ought not be altered.
Note that there are several problems and some of the examples probably won't
work. I've fixed these for the next release. gmxdemo should work, but others
may not.
-Justin
> Best,
> Majid
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
> *Sent:* Sun, February 13, 2011 9:30:52 AM
> *Subject:* Re: [gmx-users] Output of Gromacs Demo
>
>
>
> majid hasan wrote:
> > I have attached the output of demo, and another Okay, I just ran the demo
>and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and
>here is what I got.
> >
> > You seem to have the DISPLAY variable is set, so we will pop up a window
>with the output of the pdb2gmx program
> > Press <enter>
> > Starting pdb2gmx
> > [1] 28221
> > output.pdb2gmx: Permission denied
> > pdb2gmx finished
> > Press
><enter>###################################################################
> > [1] Done xterm -title pdb2gmx -sb -e tail +0f
> >
> > Then it ran genbox, gompp, and mdrun in the end (I am not totally sure of
> it
>as I forgot the whole list of programs, if you need complete list, let me
>know,
>and I'll post it).
> > I got similar output after every program. I also ran the files from
>"tutor/water" folder, but I got the "Permission denied" message. >
>
> If you installed Gromacs in the default location (/usr/local/gromacs) you
> need
>administrative privileges to write files to this directory and any
>subdirectory
>of it. Thus either issue the demo commands as sudo or install Gromacs
>elsewhere. Note, too, that there are plenty of other tutorials for learning
>Gromacs in addition to the demo:
>
> http://www.gromacs.org/Documentation/Tutorials
>
> -Justin
>
> >
> >
> > ------------------------------------------------------------------------
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>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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