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Thank you very much Tsjerk,<div><br></div><div>I under cosine content much better now.</div><div><br></div><div>When you means "that only makes sense for one Pc, the analysis is thus performed per component", could you mind to explain more?</div><div><br></div><div>I did the cosine content analysis with the following command "<span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); "> /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8"</span></div><div><br></div><div>So, I got eight rows in my result as follows:</div><div><br></div><div><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 1 0.602921</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(
42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 2 0.011185</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 3 0.0659901</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 4 0.425943</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family:
Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 5 0.204306</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 6 0.439315</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 7 0.0288551</span><br style="line-height: 17px; color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; background-color: rgb(255, 255, 255); "><span style="color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial,
sans-serif; line-height: 17px; background-color: rgb(255, 255, 255); ">> > 8 0.0830944</span> </div><div><br></div><div>Do you mean I should only look at the first row? </div><div><br></div><div>Or should I change the command from eight to one as follows: "<span style="background-color: rgb(255, 255, 255); color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; font-size: 10pt; "> </span><span style="background-color: rgb(255, 255, 255); color: rgb(42, 42, 42); font-family: Tahoma, Verdana, Arial, sans-serif; line-height: 17px; font-size: 10pt; ">/usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 1"</span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; ">When you said I should perform the analysis per component, do you mean I should also consider row 2-8 above? If yes, could you teach me how to interpret it too?</span></div><div><span style="font-size
: 10pt; "><br></span></div><div><span style="font-size: 10pt; ">Sorry to have so many questions, hope you don't mind.</span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; ">Best regards & many many thanks in advanced,</span></div><div><span style="font-size: 10pt; "><br></span></div><div>Catherine</div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; "> </span></div><div><br><div><div id="SkyDrivePlaceholder"></div>> Date: Thu, 12 Apr 2012 11:53:25 +0200<br>> Subject: Re: [gmx-users] What is an acceptable cosine content values?<br>> From: tsjerkw@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>>
Hi Catherine,<br>> <br>> > When we use cosine content to determine if our simulation are converged or<br>> > not, should I<br>> <br>> You can't use the cosine content to determine if a simulation is<br>> converged. You can only use it to determine whether the simulation is<br>> not converged, which is quite a different thing.<br>> <br>> > (1) sum all the first three principal components together or examine<br>> > individually?<br>> <br>> Determination of the cosine content is done by means of fitting, and<br>> the cosine content can be regarded a correlation coefficient, which is<br>> one for a perfect fit and 0 for no fit. That only makes sense for one<br>> pc. The analysis is thus performed per component.<br>> <br>> > (2) If I expect the first 10 ns is the equilbrium period, while the other 20<br>> > ns as the production period. Should I include all 30 ns of trajectory to<br>> > the analys
is or should I just include the last 20 ns trajectory to the<br>> > analysis?<br>> <br>> No, you should perform the analysis on the part you intend to use for<br>> all analysis.<br>> <br>> > (3) Let's if I got the PC1 as low as 0.3, can I still claim the trajectories<br>> > are converged?<br>> <br>> No. You can claim that the cosine content is low, but that is not the<br>> same as being converged.<br>> <br>> > (4) Did you comes across that when you increase the simulation time, the<br>> > cosine content values of the first three principal components did not goes<br>> > down but increased?<br>> <br>> May very well happen. Especially if the system tips over to a<br>> previously unexplored region of conformational space due to a<br>> conformational change or internal rearrangement.<br>> <br>> Cheers,<br>> <br>> Tsjerk<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.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></div></div> </div></body>
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