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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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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