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

Justin Lemkul jalemkul at vt.edu
Wed May 30 13:49:01 CEST 2018

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

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