Hi Tsjerk, Thanks for your mails and for sharing valuable insight in current discussion topic.
B.Nataraj On Wed, 29 Nov 2006 14:28:17 +0100, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Now the only reason that I did (briefly) read the paper you linked, > was because the subject interested me ;) Apparently, they did not > state which subset of Ca atoms they used. However, you can only make a > comparison like that if the sets of atoms included in the selection > are the same. Otherwise, you'd have a nice example of comparing apples > and oranges in a very improper manner. You might want to contact the > authors, or determine yourself which Ca atoms correspond between the > proteins. Now, to calculate the RMSIP, you need eigenvectors of equal > length, by definition. For such analysis to make sense, you also need > correspondence between the elements of the eigenvectors, i.e. the > atoms used for the analysis have to correspond. > > Please note that the article shows that 2 ns is not enough for > simulations to have converged. You really want to do better than that > (and check the cosine content of the first pc's). > > Cheers, > > Tsjerk > > On 11/29/06, raja <[EMAIL PROTECTED]> wrote: > > 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 > > > > > -- > 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 - Same, same, but differentÂ… _______________________________________________ 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
