<div>Dear Tsjerk :</div> <div>Thank you very much!<BR><BR><B><I>Tsjerk Wassenaar <tsjerkw@gmail.com></I></B> 写道：</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Xi Zhao,<BR><BR>Please find attached a .csh script you can use to calculate the rmsip.<BR>The script is of the hand of Isabella Daidone, now in Heidelberg.<BR><BR>Note that for a set of 'equal' simulations there is a spread in the<BR>values you obtain for the RMSIP (i.e. it's not an absolute measure of<BR>equality unless you have full convergence of your simulations). If you<BR>want to use the RMSIP to really compare simulations check our paper in<BR>JCC 27 p. 316 (2006).<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>On 9/18/06, xi zhao <ZHAOXIITC2002@YAHOO.COM.CN>wrote:<BR>> Based on the essential dynamics analysis, the similar of the internal<BR>> fluctuations in may simulation systems was evaluated by comparing principal<BR>> subspace first
10 eigenvectors) of each structural trajectory by using the<BR>> root mean square inner product(RMSIP).<BR>> Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. &<BR>> Berendsen, H. J. A kinetic model for the internal motions of proteins:<BR>> diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.<BR>><BR>> Mark Abraham <MARK.ABRAHAM@ANU.EDU.AU>写道：<BR>> 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<BR>> http://www.gromacs.org/mailing_lists/users.php<BR>><BR>><BR>><BR>> ________________________________<BR>> 雅虎免费邮箱-3.5G容量，20M附件<BR>><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<BR>> http://www.gromacs.org/mailing_lists/users.php<BR>><BR>><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar,
Ph.D.<BR>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>Dept. of Biophysical Chemistry<BR>University of Groningen<BR>Nijenborgh 4<BR>9747AG Groningen, The Netherlands<BR>+31 50 363 4336<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</BLOCKQUOTE><BR><p> 
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