Fw: [gmx-users] Output of Gromacs Demo

[Justin A. Lemkul]

majid hasan wrote:
> I have attached the output of "demo", and "water" with the message.
> 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 (conf.gro, topol.top) from "tutor/water" folder, but I got the "Permission denied" message. 
> 
> ubuntu:/usr/share/gromacs/water/>./conf.gro
> ./conf.gro: Permission denied
> 

First of all, conf.gro is not an executable, so trying to execute it isn't going 
to do anything.  All of this is a result of the fact that you don't have 
permission to write files (at the very least) in this system-wide directory.

-Justin

> I got same output for other files like topol.top etc. 
> 
> Thanks,
> Majid
> 
> 
> 
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-- 
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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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