Thank you for your advise!<BR><BR><B><I>raja <raja_28@fastmail.us></I></B> дµÀ£º <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">HI Zhao,<BR>To compute RMSIP, you have to compute eigenvector using gromacs utility<BR>program then from that trajectory you can compute RMSIP using a script<BR>which I got from Tsjerk Wassenaar from this list. You can appraoch him.<BR><BR>Regards,<BR>B.Nataraj<BR><BR><BR>On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao"<BR><ZHAOXIITC2002@YAHOO.COM.CN>said:<BR>> Based on the essential dynamics analysis, the similar of the internal<BR>> fluctuations in may simulation systems was evaluated by comparing<BR>> principal subspace first 10 eigenvectors) of each structural trajectory<BR>> by using the root mean square inner product(RMSIP). Amadei, A.,<BR>> de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J.<BR>> A kinetic model for the internal
motions of proteins: diffusion between<BR>> multiple harmonic wells. Proteins. 1999. 35, 283-292.<BR>> <BR>> <BR>> Mark Abraham <MARK.ABRAHAM@ANU.EDU.AU>дµÀ£º xi zhao wrote:<BR>> > Dear Gromacs users:<BR>> > I am a new gromacs user, I want ro calculate r.m.s.i.p<BR>> > for exploring similar in motions of two different<BR>> > proteins, I need a script or tools to calculate it. I<BR>> > need your help!<BR>> <BR>> I don't know what r.m.s.i.p is. If you want to get help, please define<BR>> carefully what you are trying to do - even a link to a journal article<BR>> might work. Please read carefully the gromacs manual section that<BR>> describes what the utility programs do, in case one of them does it.<BR>> <BR>> Mark<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<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>> <BR>> <BR>> ---------------------------------<BR>> ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ<BR>-- <BR>raja<BR>raja_28@fastmail.us<BR><BR>-- <BR>http://www.fastmail.fm - I mean, what is it about a decent email service?<BR><BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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></BLOCKQUOTE><BR><p> 
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