<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>Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.</div><div><br></div><div>Best,</div><div>Majid</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sun, February 13, 2011 9:30:52 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Output of Gromacs Demo<br></font><br>
<br><br>majid hasan wrote:<br>> I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got.<br>> <br>> 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 from "tutor/water" folder, but I got the "Permission denied" message. <br>> <br><br>If you installed Gromacs in the default location (/usr/local/gromacs) you need administrative privileges to write files to this directory and any subdirectory of it. Thus either issue the demo commands as sudo or install Gromacs elsewhere. Note, too, that there are plenty of other tutorials for learning Gromacs in addition to the demo:<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/Tutorials">http://www.gromacs.org/Documentation/Tutorials</a></span><br><br>-Justin<br><br>> <br>> <br>> ------------------------------------------------------------------------<br>> Looking for earth-friendly autos?<br><span>> Browse Top Cars by "Green Rating" <<a target="_blank"
href="http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI">http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI</a>-> at Yahoo! Autos' Green Center.</span><br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank"
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