Re: [gmx-users] Output of Gromacs Demo

[majid hasan]

Okay, thanks. I will install it again in some other directory. 

Majid




From: Justin A. Lemkul 
To: Gromacs Users' List 
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 
> *To:* Discussion list for GROMACS users 
> *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 
>  > 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 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
> 
>  >
>  >
>  > 
>  > Looking for earth-friendly autos?
>>  Browse Top Cars by "Green Rating" 
><http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI->
>> at Yahoo! Autos' Green Center.
>  >
> 
> -- 
> 
> 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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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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Re: [gmx-users] Output of Gromacs Demo

[Justin A. Lemkul]

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 
*To:* Discussion list for GROMACS users 
*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 
 > 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 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

 >
 >
 > 
 > Looking for earth-friendly autos?
 Browse Top Cars by "Green Rating" 
<http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI-> 
at Yahoo! Autos' Green Center.

 >

-- 

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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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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Re: [gmx-users] Output of Gromacs Demo

[majid hasan]

Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.

Best,
Majid




From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
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 
> 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 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

> 
> 
> 
> Looking for earth-friendly autos?
> Browse Top Cars by "Green Rating" 
><http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI->
> at Yahoo! Autos' Green Center.
> 

-- 

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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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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Re: [gmx-users] Output of Gromacs Demo

[Justin A. Lemkul]

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 
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 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





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




--


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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Re: [gmx-users] Output of Gromacs Demo

[majid hasan]

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 
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 from 
"tutor/water" folder, but I got the "Permission denied" message.  


 

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demo_contents_1.odt
Description: application/vnd.oasis.opendocument.text
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Re: [gmx-users] Output of Gromacs Demo

[Tsjerk Wassenaar]

Hi Majid,

Check whether you have writing permissions where you're doing the demo.

Cheers,

Tsjerl

On Feb 13, 2011 6:14 AM, "TJ Mustard"  wrote:

 Majid,


 Can you post the exact executions you did.



ie

grompp ..

mdrun ..



This will help alot.

On February 12, 2011 at 7:29 PM majid hasan  wrote:
> Dear All, > I in...

TJ Mustard
Email: musta...@onid.orst.edu

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Re: [gmx-users] Output of Gromacs Demo

[TJ Mustard]

  

  
Majid,




Can you post the exact executions you did.

 

ie

grompp ..

mdrun ..

 

This will help alot.





  
   On February 12, 2011 at 7:29 PM majid hasan  wrote:
  

  

  
Dear All,
  

  
I installed the gromacs on Ubuntu, and ran the demo. But every time it produces an output file, I get this error: "output.pdb2gmx: Permission denied.", so I can't view the output. I am also unable to locate the .trr file, which is supposed to be the ultimate output of demo. Could anyone please tell me what do I have to do avoid this error, and how do I get to .trr file?
  

  
Thanks,
  

  
Majid
  

 

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TJ Mustard
Email: musta...@onid.orst.edu
  

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[gmx-users] Output of Gromacs Demo

[majid hasan]

Dear All,

I installed the gromacs on Ubuntu, and ran the demo. But every time it produces 
an output file, I get this error: "output.pdb2gmx: Permission denied.", so I 
can't view the output. I am also unable to locate the .trr file, which is 
supposed to be the ultimate output of demo. Could anyone please tell me what do 
I have to do avoid this error, and how do I get to .trr file?

Thanks,
Majid



 

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