Hi,
On Thursday, 31. July 2008, sunita gupta wrote: > hi, all > > 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 relevant take a look at g_covar and g_anaeig in the manual. With g_covar you can calculate the (mass weighted) eigenvectors/ eigenvalues of your simulation, and this can be analysed further with g_anaeig, i think you mean the the RMSF fluctuations per atom of the eigenvectors which can be calculated with g_anaeig -rmsf > > Thanking in Anticipation greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
