[gmx-users] Permissions Problems with a New Installation

Stephen P. Molnar, Ph.D. s.molnar at sbcglobal.net
Sun Apr 8 16:34:35 CEST 2007

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.

Stephen P. Molnar, Ph.D.	        Life is a fuzzy set
Foundation for Chemistry		Stochastic and multivariate

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