Hi Tsjerk, Thanks for your reply. My purpose of calculating matrix of innerproduct is for calculation RMSIP (root mean square inner product) using a script (provided by you some month earlier). And I have found some references, showing comparison of RMSIP between more than two simulated systems consists of different proteins. How they could do it for whole protein? Since no indication of specific atoms selection in those reference pertaining to RMSIP calculation between the proteins.
For example, this one reference which is readily available to download “Native-state dynamics of the ubiquitin family: implications for function and evolution” J R Soc Interface. 2005 Mar 22;2(2):47-54 http://www-jackson.ch.cam.ac.uk/Jackson_papers_files/2006_Marianayagam_Interface_UBQ.pdf I want to do similar analysis. Kindly reply me. B.Nataraj On Wed, 29 Nov 2006 11:30:00 +0100, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Do the covariance analysis on a subset of your atoms, which is equal > in both structures, using index files. > > Cheers, > > Tsjerk > > On 11/29/06, raja <[EMAIL PROTECTED]> wrote: > > Hi gmxions, > > I like compute matrix of inner products using the command g_anaeig > > between eigenvector trr file of two different protein. When I do it, it > > shows error of dimension mismatch between two trr file, the error is > > understandable by me since eigen vectors computed for these two proteins > > are of different residue length, How to overcome this issue? Kindly > > reply me. > > > > With thanks! > > B.Nataraj > > -- > > raja > > [EMAIL PROTECTED] > > > > -- > > http://www.fastmail.fm - Access all of your messages and folders > > wherever you are > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - One of many happy users: http://www.fastmail.fm/docs/quotes.html _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
