<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>Okay, thanks. I will install it again in some other directory.&nbsp;</div><div><br></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 &lt;jalemkul@vt.edu&gt;<br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List &lt;gmx-users@gromacs.org&gt;<br><b><span style="font-weight: bold;">Sent:</span></b> Sun, February 13, 2011 1:39:16 PM<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>&gt; Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.<br>&gt; <br><br>You normally don't want to do any work within the Gromacs installation directories.&nbsp; For the demo, I suppose it's alright, but sudo is really just a work-around to write in directories which normally ought not be altered.<br><br>Note that there are several problems and some of the examples probably won't work.&nbsp; I've fixed these for the next release.&nbsp; gmxdemo should work, but others may not.<br><br>-Justin<br><br>&gt; Best,<br>&gt; Majid<br>&gt; <br>&gt; ------------------------------------------------------------------------<br>&gt; *From:* Justin A. Lemkul &lt;<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;<br>&gt; *To:* Discussion list for GROMACS users &lt;<a ymailto="mailto:gmx-users@gromacs.org"
 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt; *Sent:* Sun, February 13, 2011 9:30:52 AM<br>&gt; *Subject:* Re: [gmx-users] Output of Gromacs Demo<br>&gt; <br>&gt; <br>&gt; <br>&gt; majid hasan wrote:<br>&gt;&nbsp; &gt; 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>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program<br>&gt;&nbsp; &gt; Press &lt;enter&gt;<br>&gt;&nbsp; &gt; Starting pdb2gmx<br>&gt;&nbsp; &gt; [1] 28221<br>&gt;&nbsp; &gt; output.pdb2gmx: Permission denied<br>&gt;&nbsp; &gt; pdb2gmx finished<br>&gt;&nbsp; &gt; Press &lt;enter&gt;###################################################################<br>&gt;&nbsp; &gt; [1]&nbsp; &nbsp; Done&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; xterm -title pdb2gmx -sb -e tail +0f<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; 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>&gt;&nbsp; &gt; I got similar output after every program. I also ran the files from "tutor/water" folder, but I got the "Permission denied" message.&nbsp; &gt;<br>&gt; <br>&gt; 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.&nbsp; Thus either issue the demo commands as sudo or install Gromacs elsewhere.&nbsp; Note, too, that there are plenty of other tutorials for learning Gromacs in addition to the demo:<br>&gt; <br><span>&gt; <a target="_blank"
 href="http://www.gromacs.org/Documentation/Tutorials">http://www.gromacs.org/Documentation/Tutorials</a></span><br>&gt; <br>&gt; -Justin<br>&gt; <br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; ------------------------------------------------------------------------<br>&gt;&nbsp; &gt; Looking for earth-friendly autos?<br>&gt;&gt;&nbsp; Browse Top Cars by "Green Rating" <br><span>&gt; &lt;<a target="_blank" href="http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI">http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI</a>-&gt; at Yahoo! Autos' Green Center.</span><br>&gt;&nbsp; &gt;<br>&gt; <br>&gt; -- ========================================<br>&gt; <br>&gt; Justin A. Lemkul<br>&gt; Ph.D. Candidate<br>&gt; ICTAS Doctoral Scholar<br>&gt; MILES-IGERT Trainee<br>&gt; Department of Biochemistry<br>&gt; Virginia Tech<br>&gt;
 Blacksburg, VA<br>&gt; jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a><span> &lt;<a target="_blank" href="http://vt.edu">http://vt.edu</a>&gt; | (540) 231-9080</span><br><span>&gt; <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>&gt; <br>&gt; ========================================<br>&gt; -- gmx-users mailing list&nbsp; &nbsp; <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> &lt;mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br><span>&gt; <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>&gt; Please search the archive at <a target="_blank"
 href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>&gt; Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> &lt;mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>&gt;.<br><span>&gt; Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br>&gt; <br>&gt; ------------------------------------------------------------------------<br><span>&gt; Expecting? Get great news right away with email Auto-Check. &lt;<a target="_blank"
 href="http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html">http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html</a>&gt;</span><br>&gt; Try the Yahoo! Mail Beta. &lt;<a href="http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html" target="_blank">http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html</a>&gt;<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]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list&nbsp;
 &nbsp; <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></div><div style="position:fixed"></div>


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