[gmx-users] Re: covariance matrix

Hi Tsjerk, You are absolutely right! :-) Thanks for your help!  Regards, Maki Yoshisawa Celebrate Yahoo! JAPAN 10th Anniversary ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)

[gmx-users] covariance matrix

Hi! I am not quite sure I have understood the way the ASCII version of the covariance matrix (-ASCII option of g_covar) has been constructed... In my test system I have 3 atoms - this will give a 9X9 cov. matrix. In the help of g_covar the order the covar.dat file is: first row: x1x1 x1y1 x1z1  se

[gmx-users] principal component analysis

Dear David, thank you ver much! As a matter of fact, g_angle (3.3) is working perfectly well! It was a stupid error of mine!! Sorry for the inconvenience... Best wishes! Maki Yoshizawa     Celebrate Yahoo! JAPAN 10th Anniversary ___ gmx-users mailing l

Re: [gmx-users] principal component analysis

Dear David, thank you very much for your reply! Indeed I have used -type dihedral. Could it be, the problem lies in the [].tpr and [].xtc files? I mean, which subset of atoms must I choose in those files? (This very part of the previous discussion was obscure to me!) Best wishes! Maki Yoshiza

[gmx-users] principal component analysis

Hello, I would like to use PCA analysis in the dihedral space. Despite having read the topics related to this issue in the GROMACS page I am not quite sure how to accomplish this :-) The -or option in the g_angle (version 3.3) seems not to be working. I am already using an index file as sugested i