VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Mar 07 2017 - 19:49:31 CST

Thank you for your reply.------------------------------------------------------------------From:Bennion, Brian <bennion1_at_llnl.gov>Time:2017 Mar 8 (Wed) 02:07To:孙业平 <sunyeping_at_aliyun.com>; vmd-l <vmd-l_at_ks.uiuc.edu>Subject:RE: vmd-l: Usage of the Orient package
Hello The tcl code for this package is easily modified.  I wanted to know the angle between system z-axis and the molecules principle axis.  I just stuck an extra variable to catch
 the angle after it was calculated and spit it out at the end of the analysis. Brian  From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
On Behalf Of sunyeping
Sent: Monday, March 06, 2017 19:32
To: vmd-l <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Usage of the Orient package Dear all, By using Orient package I can draw the three prinicipal axes and rotate the molecule to align it to the x, y, z direction. And we can also get the variable I, the inertia tensor.
 However, how could I get the information of the principal axes? For example, I have a MD trajectory of a protein and I wish to get the coordinates of a principal axis ( represented by the x, y, z coodinates of two points: the mass center and another point
 in the principal axis) of the protein in each frame, then how should I calculate for that? Best regards, Yeping Sun