[gmx-users] angle distribution between a vector and Z axis

Christopher Neale chris.neale at alum.utoronto.ca
Sun Apr 19 03:52:23 CEST 2015

You can get the coordinates of all P and N atoms with g_traj and then write an awk script to process the output (determine the angles and make the histogram).

But if g_angle in gromacs 5 can do it, then why not just use that? Many analysis programs will take a .gro file for the -s option, and if you do need a gmx 5 .tpr then I presume that you can make one.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Marzieh Saeedi Masineh <msaeedi at mail.kntu.ac.ir>
Sent: 18 April 2015 10:58
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] angle distribution between a vector and Z axis


I simulated a DMPC lipid bilayer. I want to calculate the distribution of angle between phosphorus - nitrogen vector (P-N vector) and Z axis. Is there any command to calculate angle distribution between a vector and an axis? My Gromacs version is 4.5.4.

I searched and found gangle command for Gromacs version 5 that can calculate this angle. How can I calculate for 4.5.4 version?

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