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

[Justin Lemkul]

On 2/14/17 9:31 AM, Ezequiel Frigini wrote:
> Hi Justin, thanks for answering my question!
>
> But I think those two packages do not serve me. Because "g_sgangle"
> calculates the angle only for a group of 2 or 3 atoms. I have 120 phosphors
> and 120 nitrogen. Therefore, I have 120 PN vectors. The other package,
> g_angle, requires 3 atoms to calculate the angle.
>

You have 120 pairs of 2 atoms, therefore 120 calculations to perform.  What 
you're probably interested in is the average P-N angle with respect to z, as 
well as their distribution.  Loop over 120 calculations and you have a wealth of 
information that can be compared to experimental values.

-Justin

> I need to calculate the angle that the 120 PN vectors make with respect to
> the normal one of the lipid bilayer.
>
> If I'm wrong I could correct myself!
>
> Thank you again!
>
> ************************************************************
> Ezequiel Nazareno Frigini
> Lic. en Biología Molecular
> Grupo de Bioinformática Estructural
> bios.unsl.edu.ar
>
> Instituto de Matemática Aplicada San Luis, IMASL.
> Universidad Nacional de San Luis - CONICET.
> Calle Ejercito de Los Andes 950
> D5700HHW San Luis. Argentina.
>
> Tel: +54 266 4520300 int. 3046
>
> ************************************************************
>

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

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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