Hi, A displacement is not a fluctuation. Displacement is also relational, so you'll have to specify with respect to what. Likely you'd interpret displacement with respect to the mean structure, which by definition is at zero on a given principl axis. But in that case, the displacement is more commonly referred to as the projection (option -proj of g_anaeig) on that axis. The rmsf is the standard-deviation (well, more correctly the square root of the second moment) of the displacement/projection.
When using covariance analysis in MD, make sure first to understand what it is; read some texts from statistics to get a good grasp. Cheers, Tsjerk On Fri, Aug 1, 2008 at 10:05 AM, Bert de Groot <[EMAIL PROTECTED]> wrote: > sunita gupta wrote: >> >> Hello >> >> I have a query that how to do PCA which further includes *plotting the >> displacement of each C-alpha along first eigenvector having largest >> eigenvalue*. I read in many articles that this can be done using gromacs. I >> did my MD simutaion using charmm forcefield and NAMD. I have converted my >> *dcd file trr* and using *g_covar *covariance analysis. But i am not getting >> anything regarding displacement calculation.... >> >> In GROMACS 3.1 manual their is an option of *-disp* is given with >> *g_anaeig* command...but in 3.2 and 3.3. no such information is given and >> its considering as invalid argument. >> >> Also someone mailed me that calculating the displacement along >> eigenvectors is same as rmsf (root mean square fluctuation) and it can be >> calculated using -rmsf option in g_anaeig commant......Kindly help me in >> this regard and clear my doubts... >> > > g_anaeig -rmsf > seems a perfectly valid suggestion to me. What's your doubt? > > > Bert > > ______________________________________ > Bert de Groot, PhD > > Max Planck Institute for Biophysical Chemistry > Computational biomolecular dynamics group > Am Fassberg 11 > 37077 Goettingen, Germany > > tel: +49-551-2012308, fax: +49-551-2012302 > http://www.mpibpc.mpg.de/groups/de_groot > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 search the archive at http://www.gromacs.org/search before posting! 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
