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

delara aghaie d_aghaie at yahoo.com
Sat Jun 2 10:15:33 CEST 2018

  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

    On Wednesday, 30 May 2018, 16:19:18 GMT+4:30, Justin Lemkul <jalemkul at vt.edu> wrote:  

On 5/30/18 4:06 AM, delara aghaie wrote:
> Dear Gromacs users
> My simulation box contains dppc lipid bilayer containing a membrane protein.
> I want to calculate the angle between P-N in dppc head group and the bilayer normal (z-axis).
> 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 definition.
> 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 calculation.

Use gmx gangle -g2 z



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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