Re: Fw: [gmx-users] Output of Gromacs Demo

[Tsjerk Wassenaar]

Hi Majid,

Maybe it's a good idea to find somebody around that can help you get started
with using linux. You should get acquainted with that before trying to use
some specialized software.

Cheers,

Tsjerk

On Feb 13, 2011 6:38 PM, "Justin A. Lemkul"  wrote:

majid hasan wrote: > > I have attached the output of "demo", and "water"
with the message. > I jus...
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 >
> > > > -...
> Browse Top Cars by "Green Rating" <
> http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI->
> at Yahoo! Autos' Green Center.
>
> 
> TV dinner still cooling?
> Check out "Tonight's Picks" <
> http://us.rd.yahoo.com/evt=49979/*http://tv.yahoo.com/> on Yahoo! TV.
>
>  --  Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Schol...
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Re: 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 
Starting pdb2gmx
[1] 28221
output.pdb2gmx: Permission denied
pdb2gmx finished
Press ###
[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




Looking for earth-friendly autos?
Browse Top Cars by "Green Rating" 
 
at Yahoo! Autos' Green Center.



TV dinner still cooling?
Check out "Tonight's Picks" 
 on Yahoo! TV.




--


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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Fw: [gmx-users] Output of Gromacs Demo

[majid hasan]

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 
Starting pdb2gmx
[1] 28221
output.pdb2gmx: Permission denied
pdb2gmx finished
Press ###
[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

I got same output for other files like topol.top etc. 

Thanks,
Majid



Looking for earth-friendly autos? 
Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. 


 

TV dinner still cooling? 
Check out "Tonight's Picks" on Yahoo! TV.
http://tv.yahoo.com/

demo_contents_1.odt
Description: application/vnd.oasis.opendocument.text
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