[gmx-users] How to calculate the angle between the bilayer normal and the P−N vector?

[Justin Lemkul]

On 2/13/17 6:20 PM, Ezequiel Frigini wrote:
> Dear gromacs users,
>
> I need to calculate the angle between the bilayer normal and the P−N vector.
>
> Gathering information (but I'm not sure), I think one way to do this is:
>
> 1- Generate an index.ndx with g_selection of all the P and N of a monolayer.
>
> 2- Then use g_bundle as follows:
>
>    g_bundle -f xxx.xtc -s xxx.tpr -n index_P_N.ndx -z -na 1 -o angulo_PN.xvg
>
> I'm not sure if this is okay. Primarily if "-z" is the normal of the
> bilayer. Also, I'm not clear why "-na" should be 1.
>
> Thank you in advance!
>
>

Probably the better program to use is gmx gangle (or g_sgangle in old versions, 
as would be implied by your g_bundle command).  It has a mode to calculate the 
angle of any group using the z-axis as reference.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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