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

delara aghaie d_aghaie at yahoo.com
Wed May 30 10:21:34 CEST 2018

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.

Your help would be greatly appreciated.
Best regards

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