[gmx-users] Permissions Problems with a New Installation

[David van der Spoel]

Stephen P. Molnar, Ph.D. wrote:
> I have just upgraded my linux computer with a 64 bit AMD CPU running the 
>  64 bit openSUSW 10.2.
> 
> I installed the appropriate version of gromacs in the installer default 
> locations as the superuser without any problems.
> 
> When I run the demo as a user there appear to be permissions issues.
> 
> First of all, everytime the demo script opens a xterm window it flashes 
> and closes.
> 
> Here's what I get when the demo script gets to the grimpp module:
> 
>> generating energy minimisation parameter file...
>> em.mdp: Permission denied.
>> Starting grompp...
>> [1] 14663
>> [1]    Done                          xterm -title grompp -sb -e tail 
>> +0f output.grompp_em
>> output.grompp_em: Permission denied.
>> grompp finished
>> Press <enter>
> 
> Then the demo script ends on:
> 
>> e are finished simulating, and we are going to view the calculated
>> trajectory. The trajectory file ( .trj extension ) contains all
>> coordinates, velocities and forces of all the atoms in our system.
>>
>> The next program we are going run is ngmx. ngmx is a very simple
>> trajectory viewer.
>>
>> Once the ngmx program has been started you need to click on a few
>> buttons to view your trajectory.
>>
>> 1. Once the program has been started a dialog box shows up. Click on
>> the box on the left of the word Protein. ( This means that we want to
>> view the peptide ). Then Click on the OK Button
>>
>> 2. Now we see the edges of the box with a lines drawing of the peptide
>> we just simulated.
>>
>> 3. Select Animation in the Display menu. If you did this correctly. A
>> dialog box at the bottom of the screen appears. This dialog box is
>> used to move through your trajectory.
>>
>> 4. Click on the FastForward button (two triangles pointing to the
>> right) and watch the peptide moving.
>> -----------------------------------------------------------------
>> -----------------------------------------------------------------
>> Starting Trajectory viewer...
>> ngmx: Command not found.
>> [1] 14724
>> [1]    Exit 1                        ngmx -f cpeptide_md -s cpeptide_md
>> tutor/gmxdemo>
>>
> 
> I will be most appreciative of assistance in solving this problem as 
> permissions as a user remain a black, arcane mystery to me.
> 
> Thanks in advance.
> 
> 
> 
> 
> 
you should copy the tutorial files to your home directory first.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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