<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. </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 <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List <gmx-users@gromacs.org><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>> Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.<br>> <br><br>You normally don't want to do any work within the Gromacs installation directories. 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. I've fixed these for the next release. gmxdemo should work, but others may not.<br><br>-Justin<br><br>> Best,<br>> Majid<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Sun, February 13, 2011 9:30:52 AM<br>> *Subject:* Re: [gmx-users] Output of Gromacs Demo<br>> <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>> 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>>> Browse Top Cars by "Green Rating" <br><span>> <<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><span> <<a target="_blank" href="http://vt.edu">http://vt.edu</a>> | (540) 231-9080</span><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> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span>> <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>> Please search the archive at <a target="_blank"
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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>></span><br>> Try the Yahoo! Mail Beta. <<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>><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
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