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makson96 / Dynamics

Dynamics PyMOL Plugin
GNU General Public License v3.0
39 stars 17 forks source link

Plugin not working as normal user #77

Closed pratik-narain closed 7 years ago

pratik-narain commented 7 years ago

I compiled gromacs 5.1.3 on arch linux with mpi support and then installed pymol and this plugin as instructed in the guide. Now when I run pymol I can open the plugin only as root user. When I try to open it as normal user, it says GROMACS not detected. I tried linking gmx_mpi to gmx as suggested in an earlier post and also installing the plugin as a normal (non-root) user but nothing works. Any help is appreciated.

ghost commented 7 years ago

Hi, Can you run "gmx" command from the console as a normal user?

pratik-narain commented 7 years ago

yes. In fact I can run a whole MD simulation in gromacs from command line.

On Fri, Aug 5, 2016 at 2:57 PM, tomaszmakarewicz notifications@github.com wrote:

Hi, Can you run "gmx" command from the console as a normal user?

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ghost commented 7 years ago

The plugin should create ".dynamics" directory in your home directory. Please remove it to have clean environment. Then start PyMOL and the plugin again. If the error happens again, please attach "test_gromacs.txt" file which will appear in "~/.dynamics" directory.

pratik-narain commented 7 years ago

tried it. i am attaching the file test_gromacs.txt image

Also attached is a screenshot to show that gmx is there in the path

pratik-narain commented 7 years ago

Solved it. I just realised that I need to link gmx_mpi as gmx somewhere in PATH. So, I did it in /usr/bin and now I think its working.