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I am sorry that I did not post the link to the report. I found that sometimes these links do not work specially if they are too old. <BR>
<A href="http://lists.gromacs.org/pipermail/gmx-users/2009-March/040068.html">http://lists.gromacs.org/pipermail/gmx-users/2009-March/040068.html</A><BR>
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The result does not change with -o or -od option. I have 128 lipids (not exactly dppc though, head group is different) and water.<BR><BR>
Thanks much.<BR>
Jayeeta <BR>> Date: Thu, 11 Mar 2010 15:14:41 -0500<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] g_order 4.0.7<BR>> <BR>> <BR>> <BR>> Jayeeta Ghosh wrote:<BR>> > Dear Gromacs Users,<BR>> > I am having similar problem that was reported by Sarah about a year ago. <BR>> > I am using Gromacs4.0.7. I am using the following command to make the <BR>> > index file.<BR>> <BR>> It would be more efficient if you posted a link to the report of the issue. If <BR>> it is the problem I am thinking of, the output was not generated because of an <BR>> incorrect index file, which may or may not be the case here.<BR>> <BR>> > make_ndx -f dppc128.gro -o sn1.ndx<BR>> > > a C34<BR>> > > a C36<BR>> > > ...<BR>> > > a C50<BR>> > > del 0-2<BR>> > > q<BR>> > I am using following command to calculate the order parameter.<BR>> > g_order -n sn1.ndx -od <BR>> > I am using all other default input file names. I am only getting two <BR>> > output files: sg-ang.xvg and sk-dist.xvg, no order.xvg.<BR>> > I am not sure how to get around this.<BR>> <BR>> That's very weird, the files you're getting are the optional output, which you <BR>> haven't specified. If you add -o and -od (for both order.xvg and deuter.xvg), <BR>> is the result any different? Does your system indeed contain only lipids?<BR>> <BR>> -Justin<BR>> <BR>> > I would really appreciate any help.<BR>> > Thanks,<BR>> > Jayeeta<BR>> > // <BR>> > <BR>> > ------------------------------------------------------------------------<BR>> > Hotmail: Powerful Free email with security by Microsoft. Get it now. <BR>> > <http://clk.atdmt.com/GBL/go/201469230/direct/01/><BR>> > <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]vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> <BR>> ========================================<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR> <br /><hr />Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <a href='http://clk.atdmt.com/GBL/go/201469229/direct/01/' target='_new'>Sign up now.</a></body>
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