[gmx-users] How to define a vector for gangle command
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
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
gangle -g2 z
Justin A. Lemkul, Ph.D.
Tech Department of Biochemistry
303 Engel Hall
340 West Campus
Blacksburg, VA 24061
jalemkul at vt.edu
| (540) 231-3129
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