[gmx-users] How to define a vector for gangle command

delara aghaie d_aghaie at yahoo.com
Fri Jun 1 01:52:13 CEST 2018

On Wed, 30/5/18, Justin Lemkul <jalemkul at vt.edu> wrote:

 Subject: Re: [gmx-users] How to define a vector for gangle command
 To: gmx-users at gromacs.org
 Date: Wednesday, 30 May, 2018, 11:48
 Dear Justin
Many thanks for your reply.
My problem is not with the z axis. I use -g2 z for that as you mentioned.
I do not know how to define a vector for P-N vector.
Help me on this please.
Thanks in advance
 5/30/18 4:06 AM, delara aghaie wrote:
 Dear Gromacs users
 > My simulation box
 contains dppc lipid bilayer containing a membrane
 > I want to calculate the angle
 between P-N in dppc head group and the bilayer normal
 > We want to use the gromacs
 gangle command for this purpose.
 > The command asks us to define a vector for
 P-N, while for the axis z it does not require vector
 > I can make an index group
 containing all the P and N atoms of the dppc headgroup, but
 I do not know how to make a vector from these two endpoints
 to give it to the gangle command for angle
 Use gmx
 gangle -g2 z
 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Tech Department of Biochemistry
 303 Engel Hall
 340 West Campus
 Blacksburg, VA 24061
 jalemkul at vt.edu
 | (540) 231-3129
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