<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">I have attached the output of "demo", and "water" with the message. <br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. <style type="text/css">pre {font-family:"Liberation Serif";}p {margin-bottom:0.08in;}</style>
<pre>You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program<br>Press <enter><br>Starting pdb2gmx<br>[1] 28221<br>output.pdb2gmx: Permission denied<br>pdb2gmx finished<br>Press <enter>###################################################################<br>[1] Done xterm -title pdb2gmx -sb -e tail +0f<br><br>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).<br>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. <br><br>ubuntu:/usr/share/gromacs/water/>./conf.gro<br>./conf.gro: Permission denied<br><br>I got same output for other files like topol.top etc. <br><br>Thanks,<br>Majid<br></pre>
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