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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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