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Dear Tsjerk,<div><br></div><div>Am I correct to say the cosine content of the <span lang="EN-GB" style="font-size:12.0pt;mso-bidi-font-size:
11.0pt;line-height:115%;font-family:"Times New Roman";mso-fareast-font-family:
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AR-SA">first three principal components are as follows:</span></div><div><font face="'Times New Roman'" size="3"><span style="line-height: 18px;"><br></span></font></div><div><font face="'Times New Roman'" size="3"><span style="line-height: 18px;">PC1 : </span></font><span style="font-size: 10pt; ">0.602921</span></div><div><br></div><div><font face="'Times New Roman'" size="3"><span style="line-height: 18px;">PC2: </span></font><span style="font-size: 10pt; ">0.011185</span></div><div><font face="'Times New Roman'" size="3"><span style="line-height: 18px;"><br></span></font></div><div><font face="'Times New Roman'" size="3"><span style="line-height: 18px;">PC3: </span></font>
0.0659901 </div><div><br></div><div>As my coscont.xvg file is as follows:</div><div><br></div><div>> > @ title "Cosine content"<br>> > @ xaxis label "set / half periods"<br>> > @ yaxis label "cosine content"<br>> > @TYPE xy<br>> > 1 0.602921<br>> > 2 0.011185<br>> > 3 0.0659901<br>> > 4 0.425943<br>> > 5 0.204306<br>> > 6 0.439315<br>> > 7 0.0288551<br>> > 8 0.0830944
</div><div><br>Best regards,</div><div><br></div><div>Catherine<br><br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Tue, 10 Apr 2012 13:12:40 +0200<br>> Subject: Re: [gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file?<br>> From: tsjerkw@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hi Catherine,<br>> <br>> A converged system will yield low cosine content. But that can't be<br>> turned around! I can think of a lot of lines that don't match well<br>> with a cosine, but that are inconsistent with convergence.<br>> <br>> That said, the index in the .xvg file is the principal component<br>> index. So the projection on the first pc has a cosine content of 0.6.<br>> <br>> Cheers,<br>> <br>> Tsjerk<br>> <br>> On Tue, Apr 10, 2012 at 5:28 AM, a a <patd_2@hotmail.com> wrote:<br>> > Dear Sir/Madam,<br>> ><br>> > I used the following steps to get the cosi
ne content for my trajectories,<br>> > could you please kindly tell me how to interpret the results?<br>> ><br>> > /usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v<br>> ><br>> > /usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v<br>> > eigenvec.trr -proj<br>> ><br>> > /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8<br>> ><br>> > In the final "coscont.xvg", I found the followings:<br>> ><br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> > # This file was created Tue Apr 10 10:59:12 2012<br>> > # by the following command:<br>> > # /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8<br>> > #<br>> > # g_analyze_d is p art of G R O M A C S:<br>> > #<br>> > # Giant Rising Ordinary Mutants for A Clerical Setup<br>> > #<br>> > @ title "Cosine co
ntent"<br>> > @ xaxis label "set / half periods"<br>> > @ yaxis label "cosine content"<br>> > @TYPE xy<br>> > 1 0.602921<br>> > 2 0.011185<br>> > 3 0.0659901<br>> > 4 0.425943<br>> > 5 0.204306<br>> > 6 0.439315<br>> > 7 0.0288551<br>> > 8 0.0830944<br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> ><br>> > I read some literature quoted the first three PCs's cosine content, if<br>> > the cosine content close to zero, the trajectory is converged.<br>> ><br>> > How can I extract the first three PCs's cosine content from the above<br>> > "conscont.xvg" file? Please kindly help.<br>> ><br>> > Best regards,<br>> ><br>> > Catherine<br>> ><br>> ><br>> > --<br>&
gt; > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists<br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> <br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> * Groningen Institute for Biomolecular Research and Biotechnology<br>> * Zernike Institute for Advanced Materials<br>> University of Groningen<br>> The Netherlands<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.gromac
s.org/Support/Mailing_Lists/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/Support/Mailing_Lists<br></div></div> </div></body>
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